Effects of the two planting systems on soil fungal diversity
In this study, 561,254 sequences were generated from 15 samples obtained from 5 treatments. Base sequences with a length of 201–300 bp accounted for 97.82% of all sequences (Table S1a,b). Rarefaction curves at a similarity level of 97% indicated that the number of sequences extracted from most samples tended to plateau above 10,000. The number of sequences extracted in the test exceeded 30,000, suggesting that the sequencing data were close to saturation, sequencing depth was reasonable, and the results reflected true sample conditions (Fig. 1). The coverage of all samples was above 99.84%. The range of reads in each sample was between 34,390 and 43,510. The range of Operational Taxonomic Units (OTUs) in each sample was between 145 and 318 (Table 1).
α-Diversity comparison. Rarefaction curves for OTUs were calculated using Mothur (v1.27.0) with reads normalized to more than 30,000 for each sample using a distance of 0.03 OTU.
The analysis of alpha diversity showed that with increasing planting time, soil fungal OTUs, the Chao index, and the ACE index in TPP-treated plots increased and then decreased with time. In the VEE-IPBP-treated plots, these 3 indexes increased with time and were 56.94%, 33.81%, and 32.50% higher than those in the TPP-treated plots, respectively, after 6 years of implementation (p < 0.05). Under both planting systems, the Shannon index values of soil fungi increased and then decreased with time; however, within the same period of time, these values were 21.86% and 11.07% higher in the VEE-IPBP-treated plots than in the TPP-treated plots after 3 and 6 years, respectively. This indicated that VEE-IPBP led to greater increases in soil fungal richness and diversity than TPP (Table 1).
Comparison of soil fungal community structure between the two planting systems
Venn diagrams showed that the number of fungal OTUs that were common across samples from the TPP- and VEE-IPBP-treated plots across all planting time scales was 18 (Fig. 2). There were relatively few OTUs unique to the TPP-treated plots across all planting time scales; there were 25 and 20 in TPP13 and TPP16, respectively. There were more OTUs unique to the VEE-IPBP-treated plots across all planting time scales, with 36 and 69 for VEE13 and VEE16, respectively, and they exhibited an increasing trend. This was consistent with the trend in the total number of OTUs, indicating that VEE-IPBP altered the soil fungal community structure.
Venn diagram of the number of common and unique operational taxonomic units (OTUs). The number in the circle of petal graph represents the number of similar OTUs among samples, and the number after n represents the number of OTUs contained in a sample alone.
The analyses show that soil fungal diversity significantly increased with the duration of the experiment. There were significant differences in soil fungal abundance between the TPP- and VEE-IPBP-treated plots. At the phylum level (Fig. 3a), there were 5 fungal phyla with an abundance greater than 1% in the two planting systems: Ascomycota, Mucoromycota, Basidiomycota and Chytridiomycota. At the beginning of the experiment, in TPP10, Ascomycota were the dominant taxon, accounting for 79.21% of the fungal abundance. As the experiment progressed, Ascomycota declined rapidly, accounting for 52.70% of the abundance in TPP13 after 3 years of implementation and 7.62% in TPP16 after 6 years of implementation. Ascomycota also showed a decreasing trend in the VEE-TPB-treated plots, but it was maintained at a certain level in the later period. Ascomycota accounted for 29.70% of the abundance in VEE13 after 3 years of implementation and 25.04% in VEE16 after 6 years of implementation. Mucoromycota became the dominant taxon, accounting for 84.32% and 61.58% of the abundance in TPP16 and VEE16, respectively.
Analysis of the soil fungal community structure and composition in plots subjected to different planting systems. (A) Community structure and composition at the phylum level; (B) community structure and composition at the genus level. Taxa with an abundance of less than 1% were combined into the category ‘other’.
At the genus level (Fig. 3b), it was also shown that different plant systems altered the dominance of soil fungal taxa. At the beginning of the experiment, the genera Pseudeurotium, Cosmospora, Olpidium, and Cercophora were the dominant taxa, together accounting for 80.36% of the abundance. As the experiment progressed, the dominant taxa in the TPP-treated plots 3 years after implementation were Cylindrocarpon, Fusarium, Mortierella, and Petriella, accounting for 84.34% of the abundance. The dominant taxa in the VEE-TPBP-treated plots were Mortierella, Cosmospora, Schizothecium, and Fusarium, accounting for 79.12% of the abundance. The dominant taxa in the TPP-treated plots 6 years after implementation were Mortierella, Plectosphaerella, Fusarium, and Thielavia, accounting for 97.60% of the abundance. Among these taxa, Mortierella was the most dominant, accounting for 84.32% of the abundance. The dominant taxa in the VEE-TPBP-treated plots were Mortierella, Plectosphaerella, Bolbitius, and Fusarium, accounting for 91.23% of the abundance. Although Mortierella was again the most dominant taxon, it only accounted for 61.58% of the abundance.
Differences in soil fungal communities between the two planting systems
The results of PCoA analysis showed that the communities in the samples of the two planting systems had relatively discrete distributions across different time scales with relatively large distances between the samples (Fig. 4). As the experiment progressed, the soil fungal community diversity in the TPP- and VEE-IPBP-treated plots underwent changes. The communities in TPP13 and VEE13 after 3 years of planting showed a tendency to diverge, and after 6 years of planting, the communities in TPP16 and VEE16 had completely diverged. This indicated that differences in the planting system could influence the separation distance of the soil fungal community structure.
PCoA of the influence of two planting patterns on the diversity of soil fungi.
The results of the LEfSe analysis (Fig. 5) showed that there were 117 taxa with an LDA score greater than 2 in the 15 samples from 5 treatments that were collected at 3 time points from the 2 planting systems. The distribution of taxa across 5 taxonomic levels was as follows: 4 at the phylum level, 5 at the class level, 17 at the ordinal level, 27 at the family level, and 63 at the genus level. At the phylum level, 2 taxa of soil fungi in TPP10 exhibited relatively high relative abundance: Ascomycota and Basidiomycota. As time progressed, these highly abundant taxa underwent changes with differences between the two planting systems; 6 years after implementation, the dominant taxa were Mucoromycota in TPP16 and Blastocladiomycota in VEE16. There were significant differences (p < 0.05) between the two planting systems at all taxonomic levels.
Analysis of the differences in the composition of the fungal community between the two planting patterns (LDA scores greater than 2).
At the genus level, the taxa that differed between samples underwent changes in abundance over time and differed between planting systems. There were 12 such taxa in TPP10 (belonging to the genera Pseudeurotium, Cosmospora, Olpidium, Cercophora, and Tricholoma), 14 in TPP13 (Cylindrocarpon, Fusarium, Petriella, Podospora, and Geomyces), 6 in TPP16 (Mortierella, Thielavia, Cladorrhinum, Psathyrella, and Thermomyces), 18 in VEE13 (Schizothecium, Paramyrothecium, Entoloma, Heteroconium, and Volutella), and 13 in VEE16 (Plectosphaerella, Bolbitius, Tetracladium, Cystofilobasidium, and Ascorhizoctonia).
Relationships between environmental factors and between and among fungal communities in the two planting systems
The results of the CCA (Fig. 6) showed that planting systems and time scales explained 59.86% of the relationships between environmental factors and fungal communities. In TPP10, soil fungal taxa were mainly influenced by soil nutrients and had the highest correlation with soil available nitrogen followed by soil total phosphorus, available phosphorus, and total nitrogen and had the lowest correlation with organic matter. Soil nutrients mainly affected the genera Pseudeurotium, Cosmospora, Cercophora, and Olpidium. After 3 years of implementation, soil total potassium became the key factor and mainly influenced the taxa Pseudeurotium, Fusarium, Schizothecium, and Cylindrocarpon. After 6 years of implementation, the soil pH and moisture content became the key factors and mainly influenced Mortierella and Plectosphaerella.
Correlation between soil fungal species and soil physical and chemical properties under different planting patterns and time scales. The abbreviation “SOM” in the figure means “soil organic matter”.
To determine the functions of soil fungi associated with the changes in community structure, The FUNGuild analysis was used to perform functional predictions of soil fungi in vegetable fields under the two planting systems. Based on database annotations, the main trophic modes of soil fungi was established, including pathotrophic (P), saprotrophic (Sa), and symbiotrophic (Sy), as the 3 independent trophic modes and multitrophic modes with two or more trophic modes. The 3 independent trophic modes were further divided into 12 subgroups. A total of 78.0% of all trophic mode predictions were explained, 18.7%, 24.3%, and 0.4% of which were accounted for by the 3 independent trophic modes (P, Sa, and Sy, respectively). The 4 multitrophic modes, pathotrophic-saprotrophic (P–Sa), pathotrophic–symbiotrophic (P–Sy), saprotrophic–symbiotrophic (S–S), and fully mixed (P–S–S) trophic modes, accounted for 0.2%, 0.5%, 47.2%, and 8.7% of the predictions, respectively. Complex direct and indirect positive and negative interactions existed between fungal taxa within and between trophic modes, forming a complex network of taxonomic relationships (Fig. 7).
The relationship network of soil fungal trophic types and communities under different planting patterns.
Compared with TPP, the long-term VEE-IPBP treatment increased the proportions of the 3 independent trophic modes and 2 multitrophic modes (P–Sa and P–Sy) of soil fungi and reduced the proportions of S–S and fully mixed trophic modes. The subgroups of the trophic modes of soil fungi underwent changes accordingly. For example, among the pathotrophic fungi, plant pathogens accounted for 94.4% of fungi in the TPP-treated plots, and Cylindrocarpon and Plectosphaerella had relatively high abundances. Fungal parasites accounted for 5.0% of fungi, with Cosmospora being the main taxon. In contrast, in the VEE-treated plots, the proportions of plant pathogens were reduced to 77.6%, and Plectosphaerella and Cylindrocarpon had relatively high abundances. The proportion of fungal parasites increased to 19.3%, and Cosmospora remained the main taxon. Coprophilous fungi accounted for 42.0%, with Thielavia and Schizothecium being the dominant taxa. Soil saprophytic fungi accounted for 5.8%, with Geomyces being the dominant taxon. In contrast, in the VEE-treated plots, the abundance of Geomyces was reduced to no more than 0.7%. The dominant taxa of coprophilous fungi (accounting for 41.0%) became Schizothecium, Bolbitius, and Cercophora. For symbiotrophic fungi, only endomycorrhizae and ectomycorrhizae were detected in the two planting systems. The dominant taxa were Lecythophora and Tomentellopsis in the TPP-treated plots and Leptodontidium and Hebeloma in the VEE-IPBP-treated plots. For the S–S mode, which had a relatively high abundance overall, lower abundances of saprotrophic and ectomycorrhizal Peziza endophytic Acrostalagmus were detected in the VEE-IPBP-treated plots than in the TPP-treated plots.
Due to the multiple influences of environmental factors, nutrient sources, and biological factors, soil fungal taxa form a complex network of interactions. However, the relationship networks of the same taxa differed among planting systems. For example, in the TPP-treated plots, there were 34, 28, 57, and 7 fungal taxa that were positively correlated (+) with the 4 highly abundant and representative taxa Cylindrocarpon, Plectosphaerella, Cosmospora, and Schizothecium, respectively. There were 32, 51, 16, and 5 taxa that were negatively correlated with these representative taxa, respectively. In the VEE-IPBP-treated plots, 41, 48, 40, and 24 taxa were positively correlated with Cylindrocarpon, Plectosphaerella, Cosmospora, and Schizothecium, and 45, 37, 41, and 11 taxa were negatively correlated with these representative taxa, respectively. The fungal taxa that were the most positively (+) and most negatively (−) correlated with these representative taxa differed between the planting systems. In the TPP-treated plots, the fungal genera that were most strongly correlated with the aforementioned 4 representative fungal taxa were Ascodesmidaceae (+) and Acrophialophora (−), Mortierellaceae (+) and Psathyrella (−) Schizothecium, and Mycosphaerellaceae (−). In the VEE-IPBP-treated plots, the fungal genera that were most strongly correlated with the aforementioned 4 representative fungal taxa were Curvularia (+) and Lectera (−), Lectera (+) and Curvularia (−), Podospora (+) and Ascorhizoctonia (−), Eurotiales (+) and Acremonium (−) (see Figs. 6, 7).
Source: Ecology - nature.com
