High-Throughput Sequencing Provides Insight into Soil Fungal Community Structure and Diversity in Plant Protected Areas of Songkhla Zoo in Southern Thailand

Nitrification inhibitors that impact soil nitrifying microorganisms have been widely applied in agricultural soils to enhance the efficiency of nitrogen fertilizers. However, little is known about their combined impact with other chemical applications, such as fungicides, on soil fungi. This study specifically examined the effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP), alone or together with the fungicide iprodione, on fungi biomass and community in a typical farmland soil. Four treatments were set: (1) control of zero agrochemical applications (CK), (2) a single DMPP application (DAA), (3) repeated iprodione applications (4×IPR), and (4) combined applications of DMPP and iprodione (DAA+4×IPR). The agrochemicals were applied at the recommended intervals, and the soil samples were incubated in the dark for 28 days. During the incubation, soil sample DNA was extracted, and the effects of DMPP and iprodione applications on soil fungal internal transcribed spacer (ITS) abundances were determined with quantitative PCR (qPCR). At the end of the incubation, Illumina MiSeq method was employed to assess soil fungal community diversity and structure. DMPP application had a negligible effect on fungal ITS abundance. However, repeated iprodione applications significantly decreased fungal ITS abundances. After 28 days of incubation, the fungal ITS abundances in the 4×IPR and DAA+4×IPR treatments were 43.6 and 56.2% of that measured from the CK treatment, respectively. Shannon indices of fungal communities demonstrated the treatment-induced gradients, with the DAA+4×IPR treatment harboring the highest Shannon index. Fungal community structures following the DAA and 4×IPR treatments remained overlapping with that in the CK treatment, but repeated iprodione applications markedly enriched the family Teratosphaeriaceae. Relative to the CK treatment, fungal community structure in the DAA+4×IPR treatment was significantly changed, with the families Cephalothecaceae, Hypocreaceae, and Cordycipitaceae harboring a linear discriminant analysis value >3. DMPP application had negligible effects on soil fungal biomass, community diversity, and structure, potentially indicating that the DMPP is “bio-safe.” Conversely, repeated iprodione applications significantly decreased fungal ITS abundances. Moreover, the family Teratosphaeriaceae could be further investigated as a potential biomarker of the impacts of iprodione on soil fungi. The combined applications of DMPP and iprodione stimulated the Shannon diversity index and markedly changed soil fungal community structure.

Impacts of invasive plants on soil fungi and on above- and belowground plant diversity in temperate forests

Variation and drivers of soil fungal and functional groups among different forest types in warm temperate secondary forests

Fungal communities have been shown to be highly sensitive toward shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L.), with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L.) or spruce (Picea abies Karst.) which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure. We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal operational taxonomic units richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM) and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera. This study extends our knowledge on the impact of forest management type on general and ectomycorrhizal fungal diversity and community structure in temperate forests. High plasticity across management types but also study site specific spatial distribution revealed new insights in the ECM fungal distribution patterns.

Shift of soil fungal communities under afforestation in Nanliu River Basin, southwest China

Saline water irrigation can alleviate the shortage of freshwater resources in the northwest arid zone, but long-term saline water irrigation can damage the soil fungal community structure. To alleviate the harm caused by salinity, biochar is used as a soil amendment to improve the soil fungal community structure. To investigate the intrinsic link between biochar application and the structural diversity of fungal communities in saline soils, two irrigation water salinity levels were set:0.35 dS·m-1 (fresh water) and 8.04 dS·m-1 (saline water). At each irrigation water salinity, two levels of biochar application were set:0 t·hm-2 (no application) and 3.7 t·hm-2 (application). High-throughput sequencing results showed that compared to that under fresh water irrigation, saline water irrigation increased fungal community species diversity and decreased fungal community species richness; biochar application under saline water irrigation reduced soil fungal community species diversity and species richness. The dominant fungal phyla in the soils of each treatment were Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Rozellomycota, and Cysticercales, and the dominant genera were Gibberella, Chaetomium, Sarocladium, Stachybotrys, and Fusarium. Compared to that under freshwater irrigation, saline water irrigation significantly increased the relative abundance of Basidiomycota and Chytridiomycota and significantly decreased the relative abundance of Ascomycota and Rozellomycota. The application of biochar under saline irrigation significantly increased the relative abundance of Ascomycota and Sarocladium but significantly decreased the relative abundance of Basidiomycota, Chaetomium, and Fusarium. LEfSe analysis showed that under the condition of no biochar application, saline irrigation reduced the number of potential biomarkers of fungal communities, whereas the application of biochar under the condition of saline irrigation increased the number of potential biomarkers of fungal communities. These results indicated that the application of biochar can improve the saline soil environment and fungal community structure and provide a theoretical basis for reasonable brackish water irrigation and soil fertilization in arid areas.

Studying the impact of land-use on fungal communities and their functional groups in wetland soil can provide a theoretical basis for the protection of wetlands. The top soil (0-20 cm) samples were collected from the wetlands with Phragmites communis (PCW), wetlands with Cladium chinense (CCW), abandoned paddy fields (APF), paddy fields (PF), and corn fields (CF) in the Huixian Karst Wetland. The fungal community structure and its functional groups were analyzed using high-throughput sequencing methods and the FUNGuild database, respectively. The results showed that the Simpson and Shannon index in PF and CF were significantly higher than those in PCW and CCW. Ascomyceta was the most dominant phylum in five land-use types with the abundance of 70.60%-87.02%, followed by Rozellomycota in PCW with the abundance of 7.14% and Basidiomycota in CCW, APF, PF, and CF with the abundance of 9.70%, 5.19%, 8.13%, and 7.50%, respectively. Pleosporales was the most dominant order in PCW with the abundance of 16.47%, while Hypocreales was the dominant one in CCW, APF, PF, and CF with the abundance of 22.52%, 23.50%, 17.60, and 23.80%, respectively. Ascobolus and Archaeorhizomyces were the most dominant genera in PCW and CCW with the abundance of 6.65% and 13.44%, respectively, and Fusarium was the most dominant genus in APF, PF, and CF with the abundance of 10.22%, 10.51%, and 11.12%, respectively. Saprotroph was the main trophic mode in the Huixian wetland with the abundance of 48.67%-80.13%. The abundance of pathotroph in CF (5.39%) was higher than that in PCW (2.34%) and CCW (1.53%). Dung saprotroph-wood saprotroph and soil saprotroph were the most dominant functional groups in PCW and CCW, respectively, while animal pathogen-endophyte-lichen parasite-plant pathogen-soil saprotroph-wood saprotroph was the most dominant functional group in APF, PF, and CF. Redundancy analysis showed that both soil water content and the ratio of carbon-to-nitrogen were the main factors affecting fungal communities, and available nitrogen was the main factor affecting the functional groups. Overall, the results indicated that land-use has changed the soil fungal diversity and community structure, complicated the functional groups, and increased the risk of corn disease in the Huixian Karst wetland.

<p>Fungal community in the soil plays a central role in natural systems and agroecosystems, therefore it attracted much research interests. However, the fungal microbiota of aromatic plants, such as Salvia sclarea L., especially in trace-element (TE) polluted conditions and within the framework of phytomanagement approaches, remains unexplored. The presence of high concentrations of TE in the soil is likely to negatively affect not only microbial diversity and community structures, but also plant establishment and growth. The objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community structure and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation during two successive years, combined or not with an exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV) respectively in the rhizospheric soil and roots of S. sclarea in TE-polluted conditions. Remarkably, 69 AMF species were detected in our experimental site, belonging to 12 AMF genera. Besides, the inoculation treatment significantly shaped the fungal communities in soil, and increased the number of AMF ASVs in clary sage roots. In addition, successive years of clary sage cultivation also significantly shaped both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of clary sage grown in TE-polluted agricultural soil.</p><p><strong>Keywords</strong>: Trace Elements-polluted soils, fungal microbiota, Salvia sclarea, arbuscular mycorrhizal fungi</p>

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities

Chitinase genes isolated from plants, bacteria or fungi have been widely used in genetic engineering to enhance the resistance of crops and trees to fungal pathogens. However, there are concerns about the possible effect of chitinase-transformed plants on nontarget fungi. This study aimed at evaluating the impact of endochitinase-transformed white spruce on soil fungal communities. Endochitinase-expressing white spruce and untransformed controls were transplanted in soils from two natural forests and grown for 8 months in a greenhouse. Soil fungal biomass and diversity, estimated through species richness and Shannon and Rao diversity indices, were not different between transgenic and control tree rhizospheres. The fungal phylogenetic community structure was the same in soil samples from control and transgenic white spruces after 8 months. Soil type and presence of seedlings had a much more significant impact on fungal community structure than the insertion and expression of the ech42 transgene within the white spruce genome. The results suggest that the insertion and constitutive expression of the ech42 gene in white spruce did not significantly affect soil fungal biomass, diversity and community structure.

Understanding the relationship between soil fungal communities and soil function is vital to establish a sustainable and ecologically friendly tea (Camellia sinensis L.) cultivation. However, there is limited research on the response of soil fungal communities to tea-fungus intercropping, particularly how it is related to soil biodiversity and fertility. Here, we assessed and compared the fungal communities using a metabarcoding technique, soil properties in three plantations (1, 2, and 5 yr of tea-Pleurotus intercropping plantations), and a 5 yr chemically fertilized monoculture plantation. We obtained a total of 3493 operational taxonomic units (OTUs) from four tea plantations. Five hundred and ninety-three fungal OTUs are shared by all plantations, and the other 471 fungal OTUs are shared by three plantations. The largest number of OTUs was recorded in 5 yr tea-Pleurotus intercropped plantations (N = 2040), followed by 2 yr (N = 2024) and then 1 yr (N = 1471), while the chemically fertilized plantation recorded 1823 OTUs. Tea-Pleurotus intercropping showed a significant effect on the increased diversity of soil fungal diversity compared with the monoculture tea cultivations. Fungal groups Basidiomycota, Ascomycota, and Mortierellomycota were the most abundant taxonomic groups recorded in all soil samples. Principal coordinate analysis revealed that fungal community composition in tea-Pleurotus intercropped plantations and monoculture tea plantations was significantly different. Besides, redundancy analysis revealed that soil nutrients significantly influence soil fungal community composition. Our results demonstrate that tea-Pleurotus intercropping may offer long-term benefits to soil biodiversity and sustainable benefits in the tea plantations.

Community assembly of ectomycorrhizal fungal communities in pure and mixed Pinus massoniana forests

Effects of different long-term farmland mulching practices on the loessial soil fungal community in a semiarid region of China

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

Jatropha curcas is widely planted as a highly drought-resistant biodiesel feedstock. Curcin protein is one of the Jatropha ribosomal inactivation proteins with broad-spectrum antifungal activity that may enter the soil ecosystem as a result of large-scale Jatropha cultivation and affect fungi and various enzymatic activities in the soil. In this research, the influence of curcin protein and Jatropha planting on soil fungi was investigated, and the levels of curcin in various tissues and organs of Jatropha were measured with an enzyme-linked immunosorbent assay. It was found that the content of curcin in seed kernels reaches 2 mg/g, which is much higher than that in other tissues. After the seeds have fallen into the soil, the level of curcin in the soil rises rapidly, reaching 59.22 µg/g soil and 67.49 µg/g soil in different soil samples, respectively. It then falls by more than 99% within six days. High-throughput sequencing technology was used to study the soils treated with different concentrations of curcin, and the results of the soil fungal alpha diversity index analysis showed that the fungal communities did not change significantly, but the abundance of each fungal community changed significantly. The degree of influence of different concentrations of curcin treatment on the abundance of the soil dominant fungal community were investigated for concentrations of 0.5 μg/g, 50 μg/g and 5 μg/g, and showed that concentrations of 0.5 μg/g and 50 μg/g are more likely to change fungal community structure in soil, and with the increasing extension of the treatment time, they may be detrimental to the conservation of soil ecosystems. Internal transcribed spacer (ITS) sequencing of soil fungi from Jatropha planted and unplanted areas in four regions with different climate types showed that Jatropha planting significantly altered the soil fungal communities in each region. There was a negative impact on soil fungal communities in tropical maritime monsoon and subtropical dry and hot monsoon climates, while a positive impact was observed in subtropical monsoon and tropical highland monsoon climates due to Jatropha cultivation. In conclusion, Jatropha plantations and curcin protein have an impact on soil fungi and thereby affect the ecological system of the soil.