Soil Fungal Community Structure Research Articles

Soil Fungal Community Composition Correlates with Site-Specific Abiotic Factors, Tree Community Structure, and Forest Age in Regenerating Tropical Rainforests.

Simple SummaryRegenerating forests represent over half of all tropical forests. While regeneration processes of trees and animal groups have been studied, there is surprisingly little information about how the diversity and community composition of fungi and other microorganisms change and what ecological roles play in tropical forest regeneration. In this study, we compared the diversity and community composition of trees and soil fungi among primary forests and regenerating forests of different ages in two sampling areas in southern Costa Rica. Our study shows that while forest age has a significant influence, environmental factors, such as mesoclimate and soil chemistry, have stronger effects on both fungal and tree communities. Moreover, we observed that the more dissimilar tree communities are between any two sites, the more dissimilar the composition of fungal communities. The results presented here contribute to a better understanding of the successional processes of tropical forests in different regions and inform land use and forest management strategies, including, but not limited to, conservation, restoration, and sustainable use.Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data to compare richness and community composition along secondary forest succession in Costa Rica and assessed the potential roles of abiotic factors influencing them. We found a strong coupling of tree and soil fungal community structure in wet tropical primary and regenerating secondary forests. Forest age, edaphic variables, and regional differences in climatic conditions all had significant effects on tree and fungal richness and community composition in all functional groups. Furthermore, we observed larger site-to-site compositional differences and greater influence of edaphic and climatic factors in secondary than in primary forests. The results suggest greater environmental heterogeneity and greater stochasticity in community assembly in the early stages of secondary forest succession and a certain convergence on a set of taxa with a competitive advantage in the more persisting environmental conditions in old-growth forests. Our work provides unprecedented insights into the successional dynamics of fungal communities during secondary tropical forest succession.

Responses of the Soil Microbial Community to Salinity Stress in Maize Fields.

Simple SummarySoil microorganisms are the core of maintaining soil ecological functions. Recognition of microbial community diversity in saline soil contributes to nutrient management and crop production. Meanwhile, microbial activity is easily affected by changes in soil properties. This study addressed how the composition and diversity of bacterial and fungal communities changed under different saline conditions to identify the sensitivity of bacteria or fungi to salinity. The primary objective was to evaluate the relationship between soil’s microbial community diversity and soil’s physicochemical factors, and to explore the vital microbial predictors in salinized soil. The results showed that Firmicutes and Bacteroidetes are pivotal in salinized soil, and this finding can provide guidance for the demand for plant rhizosphere growth-promoting bacteria as a bioindicator in saline soil.To investigate the diversity and structure of soil bacterial and fungal communities in saline soils, soil samples with three increasing salinity levels (S1, S2 and S3) were collected from a maize field in Yanqi, Xinjiang Province, China. The results showed that the K+, Na+, Ca2+ and Mg2+ values in the bulk soil were higher than those in the rhizosphere soil, with significant differences in S2 and S3 (p < 0.05). The enzyme activities of alkaline phosphatase (ALP), invertase, urease and catalase (CAT) were lower in the bulk soil than those in the rhizosphere. Principal coordinate analysis (PCoA) demonstrated that the soil microbial community structure exhibited significant differences between different salinized soils (p < 0.001). Data implied that the fungi were more susceptible to salinity stress than the bacteria based on the Shannon and Chao1 indexes. Mantel tests identified Ca2+, available phosphorus (AP), saturated electrical conductivity (ECe) and available kalium (AK) as the dominant environmental factors correlated with bacterial community structures (p < 0.001); and AP, urease, Ca2+ and ECe as the dominant factors correlated with fungal community structures (p < 0.001). The relative abundances of Firmicutes and Bacteroidetes showed positive correlations with the salinity gradient. Our findings regarding the bacteria having positive correlations with the level of salinization might be a useful biological indicator of microorganisms in saline soils.

Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing.

There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50–5.00 and 2,200-m group, and fungi peaked in the pH 5.00–5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.

Soil fungal community structure and seasonal diversity following application of organic amendments of different quality under maize cropping in Zimbabwe.

Recent advocacy for Integrated Soil Fertility Management (ISFM) in smallholder farming systems in east and southern Africa show substantial evidence of increased and sustained crop yields associated with enhanced soil productivity. However, the impact ISFM on soil fungi has received limited attention, yet fungi play key roles in crop growth. Following total soil DNA extraction with ZR soil microbe miniprep kit, illumina sequencing was used to, examine the fungal communities (ITS1F) under a maize crop following co-application of organic nutrient resources including Crotalaria juncea, cattle manure and maize stover with inorganic fertilizers at three-time periods (T1-December, T2-January, and T3-February) in Zimbabwe. Ninety-five fungal species were identified that were assigned to Ascomycota (>90%), Basidiomycota (7%) and Zygomycota (1%). At T1, Ascomycota and Basidiomycota were identified across treatments, with Ascomycota attaining > 93% frequency. Fungal succession was noted and involved reduction of Ascomycota coupled by increase in Basidiomycota under the different treatments. For example at T3, Basidiomycota increased to 34% while Ascomycota declined to 66% under manure but remained unchanged in other two organics. Pre-season mineral nitrogen (N) associated with the ‘Birch effect’ apparently influenced the fungal community structure at T1 while readily available fertilizer N was critical at T2 and T3. The low-quality maize stover promoted the presence of Exophiala sp SST 2011 and this was linked to N immobilization. The impact of N addition was more pronounced under medium (manure) to low-quality (maize stover) resources. Fungi required phosphorus (P) and N for survival while their proliferation was dependent on substrate availability linked to resource quality. Interactive-forward test indicated that soil available P and N were most influential (P < 0.05) factors shaping fungal communities. Co-application of medium to high quality organic and inorganic resources show promise as a sustainable entry point towards enhancing belowground fungal diversity critical in driving nutrient supply.

Changes in soil bacterial and fungal communities in response to Bacillus megaterium NCT-2 inoculation in secondary salinized soil.

BackgroundSecondary salinized soil in greenhouses often contains excess nitrate. Inoculation of Bacillus megaterium NCT-2 with nitrate assimilation ability represents an attractive approach for soil remediation. However, the effects of NCT-2 on the structure and function of soil microbial communities have not been explored.MethodsGreenhouse experiments were carried out to investigate changes in soil properties, Brassica chinensis L. growth, bacterial, and fungal community structure and function in response to NCT-2 inoculation.ResultsThe NCT-2 inoculant significantly reduced the nitrate content in B. chinensis and inhibited the rebound of soil nitrate in the later stage. The shifts of bacterial community structure and function by NCT-2 was negligible, and a greater disturbance of soil fungal community structure and function was observed, for example the strong inhibitory effect on ectomycorrhizal fungi. These results indicated that the NCT-2 inoculant likely achieved the remediation effect in secondary salinized soil by shifting fungal community. The present findings add to the current understanding of microbial interactions in response to bacterial inoculation and can be of great significance for the application of NCT-2 inoculants in secondary salinized soil remediation.

Soil Fungal Communities and Enzyme Activities along Local Tree Species Diversity Gradient in Subtropical Evergreen Forest

The majority of studies have found that an increase in tree species diversity can increase the productivity of forest stands thanks to complimentary effects with enhanced resource use efficiency or selection effects; however, it is unclear how tree species diversity affects the soil fungal community and enzyme activities in subtropical evergreen forests. In this study, we used soil high-throughput sequencing to investigate the soil fungal community structure and diversity in the central area of tree clusters in the gradient of tree species richness formed by four possible dominant tree species (Pinus massoniana Lamb., Choerospondias axillaris Roxb., Cyclobalanopsis glauca Thunb. and Lithocarpus glaber Thunb.) in subtropical evergreen broad-leaved forest. The results showed that soil organic carbon content and total nitrogen content were significantly higher in mixed tree clusters, and that soil fungal richness and diversity increased with the increase in tree species diversity (1–3 species). Soil acid phosphatase and urease activity were also enhanced with tree species diversity (p &lt; 0.05). The relative abundance of soil symbiotic fungi (ectomycorrhizal fungi) decreased, while the relative abundance of saprotrophic fungi increased. Redundancy analysis (RDA) revealed that soil acid phosphatase activity was the main factor affecting soil fungal communities and functional guilds, and that soil water content was the main driving force behind fungal trophic modes. In subtropical forests, changes in tree species diversity have altered the soil fungal community structure and trophic modes and functions, accelerating the decomposition of organic matter, increasing nutrient cycling, and perhaps also changing the nutrient absorption of trees.

Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots.

Apple replant disease (ARD) is a common problem in major apple planting areas, and biological factors play a leading role in its etiology. Here, we isolated the bacterial strain QSB-6 from the rhizosphere soil of healthy apple trees in a replanted orchard using the serial dilution method. Strain QSB-6 was provisionally identified as Bacillus amyloliquefaciens based on its morphology, physiological and biochemical characteristics, carbon source utilization, and chemical sensitivity. Maximum likelihood analysis based on four gene sequences [16S ribosomal RNA gene (16S rDNA), DNA gyrase subunit A (gyrA), DNA gyrase subunit B (gyrB), and RNA polymerase subunit B (rpoB)] from QSB-6 and other strains indicated that it had 100% homology with B. amyloliquefaciens, thereby confirming its identification. Flat standoff tests showed that strain QSB-6 had a strong inhibitory effect on Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Fusarium oxysporum, Alternaria alternata, Aspergillus flavus, Phoma sp., Valsa mali, Rhizoctonia solani, Penicillium brasilianum, and Albifimbria verrucaria, and it had broad-spectrum antibacterial characteristics. Extracellular metabolites from strain QSB-6 showed a strong inhibitory effect on Fusarium hyphal growth and spore germination, causing irregular swelling, atrophy, rupture, and cytoplasmic leakage of fungal hyphae. Analysis of its metabolites showed that 1,2-benzenedicarboxylic acid and benzeneacetic acid, 3- hydroxy-, methyl ester had good inhibitory effects on Fusarium, and increased the length of primary roots and the number of lateral roots of Arabidopsis thaliana plantlet. Pot experiments demonstrated that a QSB-6 bacterial fertilizer treatment (T2) significantly improved the growth of Malus hupehensis Rehd. seedlings. It increased root length, surface area, tips, and forks, respiration rate, protective enzyme activities, and the number of soil bacteria while reducing the number of soil fungi. Fermentation broth from strain QSB-6 effectively prevented root damage from Fusarium. terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) assays showed that the T2 treatment significantly reduced the abundance of Fusarium in the soil and altered the soil fungal community structure. In summary, B. amyloliquefaciens QSB-6 has a good inhibitory effect on Fusarium in the soil and can significantly promote plant root growth. It has great potential as a biological control agent against ARD.

Eucalyptus Plantation Age and Species Govern Soil Fungal Community Structure and Function Under a Tropical Monsoon Climate in China.

Fungi perform crucial roles in nutrient cycles, but there is limited information on how soil fungal communities vary with stand age and tree species. Eucalyptus has been extensively planted in China, which has caused severe soil erosion and water deficiency due to short rotation management. In this study, the fungal community structure and potential function in Eucalyptus plantations with different ages (1-5+ years) and species (Eucalyptus urophylla × Eucalyptus grandis, Eucalyptus camaldulens, and Eucalyptus pellita) under a tropical monsoon climate in China were characterized by Illumina Miseq coupled with FUNGuild analysis. The results showed that the fungal alpha diversity decreased with an increase in the age of the plantation. Plantations of different ages and species formed distinct fungal communities and potential functional structures, respectively (p < 0.05), in which the age of the plantation contributed more to the variations. At high taxonomic levels, the soil fungal community changed from the dominance of orders belonging to Ascomycota (Pleosporales, Chaetothyriales, and Eurotiales) to orders belonging to Basidiomycota (Agaricales, Sebacinales, Cantharellales, and Russulales) with increasing plantation age. The community potential function shifted from the dominance of plant pathogens to a higher abundance of saprotrophs and symbiotrophs. The organic carbon of the soil was the key environmental driver to both the fungal community and potential functional structure. The results provide useful information on the importance of fungi for the management of Eucalyptus plantations.

When nanoparticle and microbes meet: The effect of multi-walled carbon nanotubes on microbial community and nutrient cycling in hyperaccumulator system

Carbon nanotubes can potentially stimulate phytoremediation of heavy metal contaminated soil by promoting plant biomass and root growth. Yet, the regulating mechanism of carbon nanotubes on the rhizosphere microenvironment and their potential ecological risks remain poorly characterized. The purpose of this study was to systematically evaluate the effects of multi-walled carbon nanotubes (MCNT) on the diversity and structure of rhizosphere soil bacterial and fungal communities, as well as soil enzyme activities and nutrients, in Solanum nigrum L. (S. nigrum)-soil system. Here, S. nigrum were cultivated in heavy metal(loid)s contaminated soils applied with MCNT (100, 500, and 1000 mg kg-1 by concentration, none MCNT addition as control) for 60 days. Our results demonstrated more significant urease, sucrase, and acid phosphatase activities in MCNT than in control soils, which benefit to promoting plant growth. Also, there were significant reductions in available nitrogen and available potassium contents with the treatment of MCNT, while the organic carbon and available phosphorus were not affected by MCNT application. Notably, the alpha diversity of bacterial and fungal communities in the MCNT treatments did not significantly vary relative to control. However, the soil microbial taxonomic compositions were changed under the application of MCNT. Compared to the control, MCNT application increased the relative abundances of the Micrococcaceae family, Solirubrobacteraceae family, and Conexibacter genus, which were positively correlated with plant growth. In addition, the non-metric multidimensional scaling (NMDS) analysis revealed that the community structure of bacterial and fungal communities did not significantly change among all the treatments, and bacterial community structure was significantly correlated with soil organic carbon. At the same time, sucrase activity had the highest relation to fungal community structure. This study highlighted soil microbes have strong resistance and adaptation ability to carbon nanotubes with existence of plants, and revealed linkage between the rhizosphere microenvironment and plant growth, which well improved our understanding of carbon nanotubes in heavy metal phytoremediation.

Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China.

Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.

Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest.

Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha–1 yr–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO3––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.

Novel approaches of regulating soil micro-ecological environment based on modified biochar in plastic greenhouse

Soil fungal community structure was an important indicator that affects soil nutrition and sustainable farming. This research explored how the modified biochar affected the structure of soil fungal community in plastic greenhouses and the correlation between soil environmental factors and structure changes of the fungal community. In terms of field experiments, we studied how the modified biochar affected fungal diversity and physicochemical characteristics of the soil. Compared to the control group, the modified biochar significantly increased microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), organic carbon (SOC), microbial quotient (qMB), soil moisture content, and total nitrogen (TN) content. Diversity index research indicated that modified biochar significantly raises the Shannon index, ACE index and OTU number of the fungal community. The fungal phylum level was analyzed to find that the modified biochar greatly raised Ascomycota in the dominant fungal population by 13.97%, and at the same time significantly reduced the Mucoromycota, unclassified_d__Fungi and Basidiomycota decreased by 65.75%, 81.87% and 60.85%, respectively. From the analysis of fungal genus, the application of modified biochar into the soil increased the relative abundance of Aspergillus and norank_c__Leotiomycetes, among which Aspergillus increased by 678.44%. The test results also show that, the modified biochar reduced Fusarium, norank_p__Mucoromycota, Coniochaeta, Myrothecium, unclassified_o__Hypocreales and unclassified_f__Pyronemataceae by 33.12%, 73.24%, 25.59%, 41.45%, 39.13% and 82.42%, respectively. Redundancy analysis (RDA) and Mantel test analysis showed that soil MBC, MBN, pH, TN and SOC may be important related factors affecting the structure of fungal community. This research provides a theoretical basis and technical approach for the directional regulation and sustainable farming of the soil micro-ecological environment of the modified biochar in plastic greenhouses.

Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan

Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investigated the trend in co-occurrence network structure of soil fungal communities at 11 elevation levels along a 2300 m elevation gradient on Mt. Norikura, Japan, and identified the keystone taxa in the network, hypothesizing a progressive decline in network connectivity with elevation due to decreased plant diversity and enhanced environmental stress caused by changes in climate and soil characteristics. Our results demonstrated that network-level topological features such as network size, average degree, clustering coefficient, and modularity decreased significantly with increasing elevation, indicating that the fungal OTUs at low elevation were more closely associated and the network structure was more compact at low elevations. This conclusion was verified by the negative correlation between positive cohesion, negative cohesion and elevation. Moreover, the negative/positive cohesion ratio reached its peak value in mid-elevations with moderate environmental stress, indicating that the fungal community structure in mid-elevations was more stable than that at other elevations. We also found that the keystone taxa were more abundant at lower elevations. Furthermore, statistical analysis revealed that against a background of uniform geology, climate may play a dominant role in determining the properties and intensity of soil fungal networks, and significantly affect the abundance distribution of keystone taxa. These findings enhance understanding of the pattern and mechanism of the fungal community co-occurrence network along elevation, as well as the responses of microorganisms to climate change on a vertical scale in montane ecosystems. ImportanceExploration of the elevational distribution of microbial networks and their driving factors and mechanisms may provide opportunities for predicting potential impacts of environmental changes, on ecosystem functions and biogeographic patterns at a broad scale. Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts along elevational temperature gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Our results also suggest that higher elevations on mountains have fewer keystone taxa than low elevations. These patterns may be related to the decrease of plant diversity and the increase of environmental stress along elevation gradients.

Resilience of soil fungal community to hurricane Patricia (category 4)

Climate change is increasing the frequency and intensity of catastrophic events such as hurricanes. Soil microbial communities regulate geochemical cycles and other important ecosystem processes. How the hurricanes affect soil microbial communities and their function, however, is largely unknown. Our aim was to describe the impact of a category 4 hurricane (Patricia) on the soil fungal community structure and diversity in a Mexican tropical dry forest. Soil fungal community was inferred sequencing the ITS2 rDNA of composite soil samples taken in a time series ranging one year before and two years after the hurricane. OTU richness before the hurricane and in the first sampling after were comparable, however a 20–40% decrease in richness was observed in later sampling times. There were also taxonomic shifts associated with the disturbance, changing from a higher richness and abundance of Ascomycota fungi to greater dominance of Basidiomycota and Glomeromycota fungi post-hurricane. Arbuscular mycorrhizal fungi and plant pathogens diversity increased immediately after the hurricane but decreased in subsequent years. Approximately 7% of the soil community, primarily composed of saprotrophic fungi, persisted across the hurricane and the harsh seasonality of this ecosystem. Soil fungal community was affected by the hurricane but had function stability and resilience through years.

Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions.

Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.

Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil.

Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls’ and armadillos’ burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls’ burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities’ structures.

The diversity and co-occurrence network of soil bacterial and fungal communities and their implications for a new indicator of grassland degradation

Grassland degradation is a retrogressive successionofgrasslandvegetation, which leads to the loss of biodiversity and the degradation of ecosystem functions. Soil microbiomes play critical roles in the functioning and services of grassland ecosystems, yet little is known about how their diversity, structure and co-occurrence network characteristics respond to grassland degradation. Here, we used lllumina Miseq technique to evaluate soil bacterial and fungal communities in a meadow steppe with different degrees of degradation in Northeastern China. Our results showed that Actinobacteria, Proteobacteria, and Chloroflexi and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Zygomycota were the predominant fungal phyla. The relative abundance of taxa assigned to Actinobacteria, Gemmatimonadetes, Firmicutes, and Deinococcus-Thermus increased with increasing degradation degrees, whereas those affiliated with Acidobacteria and Nitrospirae showed a decreasing pattern. Compared to bacteria, the relative abundance of most fungal phyla decreased gradually along the degradation gradient. Bacterial Shannon diversity index possessed a similar hump pattern, while fungal diversity decreased with increasing degree of grassland degradation. Bacterial and fungal communities have different responses to grassland degradation, indicating that fungi are more sensitive to grassland degradation than bacteria. Both bacterial and fungal community structures were significantly different among the three sites. Changes in soil bacterial and fungal community structures were best explained by soil salinity and pH. Plant diversity and nitrogen concentration in aboveground plant tissues were also important factors for regulating fungal communities. Co-occurrence network analysis revealed that microbial taxa increased positive interactions and average degree to strengthen the adaptability of microorganisms to grassland degradation. These findings could enhance our understanding of the formation and maintenance of microbial community diversity in degraded grasslands and the development of a new indicator for grassland ecosystem management.

Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh

The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.

Effectively controlling Fusarium root rot disease of Angelica sinensis and enhancing soil fertility with a novel attapulgite-coated biocontrol agent

Angelica sinensis, a well-known medicinal herb in demand worldwide, is mainly cultivated in a cool high-altitude mountainous region in northwest China. Recently, due to climate change and the excessive use of chemical fertilizers, soil borne diseases are leading to severe production losses of A. sinensis. Here we developed a novel attapulgite coated with a particular biocontrol agent (APBA) and tested its efficacy for disease control of Fusarium root rot in A. sinensis. The plate confrontation experiment showed the biocontrol bacterium significant inhibited a variety of pathogenic fungi causing root rot. Five treatments were then evaluated in the field experiment: empty attapulgite carrier (AP), chemical fertilizer (CF), and organic fertilizer (OF) with or without the AP-coated biocontrol agent, respectively. These field trials demonstrated the incidence of Fusarium root rot disease was significantly reduced from 30.56% (CF) to 12.4% when the CF was combined with APBA (BICF), reaching as low as 11% when the OF was combined with APBA (BIOF). In the rhizosphere microbial community, bacterial diversity was significantly higher under the BICF than CF treatment, whereas the fungal diversity was lower in the BIOF treatment. Furthermore, the structure of both soil bacterial and fungal communities was considerably changed when APBA was applied, irrespective of its combination with CF or OF. Specifically, APBA enriched the relative abundances of beneficial genera, such as Bryobacter, Sphingomonas, Rokubacteria and (among others), whereas it diminished those of Gibberella, Fusarium, Cylindrocarpon, and Plectosphaerella which were positively correlated with the rot disease index. Redundancy analysis and Pearson correlations revealed that, besides their significant positive relationships with soil total carbon (TOC), total nitrogen (TON), organic matter (OM), total potassium (TK) and ammonium nitrogen (NH4-N), the APBA treatments for OF and CF were both dominated by Acidobacteria, Chloroflexi, Gemmatimonadetes, Actinobacteria, Rokubacteria, and Nitrospirae. Our PICRUSt functional data prediction indicated that APBA's application significantly affects the functioning of the rhizosphere's microbial community, but with more signal pathways and functions found overrepresented in the BIOF and BICF treatments. This comprehensive study suggests the application of this novel biocontrol agent can effectively suppress the incidence of root rot disease in A. sinensis, by improving soil chemical properties and altering microbial community composition in the A. sinensis rhizosphere.

Effects of short-term application of Moutai lees biochar on nutrients and fungal community structure in yellow soil of Guizhou.

In order to realize the utilization of Moutai lees and the improvement of soil fertility of yellow soil in Guizhou, a field experiment was carried out to study the effects of short-term application of Moutai lees biochar on nutrients and fungal community structure diversity of yellow soil. The results showed that the application of Moutai lees biochar increased the pH, soil organic matter (SOM), total nitrogen (TN), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), available phosphorus (AP), and available potassium (AK), while the microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) were reduced. The application of biochar significantly reduced the number of fungal OTU and community diversity. The application of biochar increased the relative abundances of Chytridiomycota and Mortierellomycota, while the relative abundance of Ascomycota was significantly reduced. Redundancy analysis (RDA) suggested that SOM, NH4+-N and NO3--N were the key factors correlated with changes in microbial community structure. Overall, the short-term application of lees biochar can not only improve the nutrient content of yellow soil, but also change the structure and diversity of soil fungal communities. More importantly, Moutai lees biochar can reduce the relative abundance of some pathogenic fungi and play the role of inhibiting the growth and reproduction of harmful plant pathogens.