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Article

Response of Yam Yield and Soil Microbial Communities to Soil Fumigation and Substrate Cultivation

by
Xi Jin
1,
Zheng Hao
1,
Yelong Song
1,
Lan Gao
1,
Fuqiang He
1,
Qingjie Li
2,* and
Aocheng Cao
3,*
1
Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Baoding 071000, China
2
State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3
Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
*
Authors to whom correspondence should be addressed.
Agriculture 2024, 14(8), 1231; https://doi.org/10.3390/agriculture14081231
Submission received: 22 June 2024 / Revised: 23 July 2024 / Accepted: 24 July 2024 / Published: 26 July 2024
(This article belongs to the Section Crop Protection, Diseases, Pests and Weeds)
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Versions Notes

Abstract

:
Soil fumigation is considered a method to control soil-borne diseases and solve crop continuous cropping obstacles. However, fumigant residues in the soil are detrimental to soil health. Though substrate cultivation is a cultivation mode that can promote plant growth, studies to date on whether substrate cultivation can replace soil fumigation for the control of soil pathogens are limited. In this study, the effects of chloropicrin fumigation (Pic) and substrate cultivation (SC) on yam growth, soil pathogens, soil nutrients, and microbial communities were demonstrated using a 2-year field experiment. The results showed that SC significantly increased the content of soil organic matter (SOM), available phosphorus, and available potassium compared with Pic. In addition, SC could effectively reduce the number of Fusarium spp. and Phytophthora spp., decrease the rate of diseased yam plants, and significantly increase the yam yield. Moreover, SC significantly increased the abundance of beneficial microorganisms such as Actinobacteriota, Acidobacteriota, and Bacillus in soil. Correlation analysis showed that yam yield exhibited a negative relation with the number of soil pathogens and a positive correlation with SOM. Our study suggests that substrate cultivation can be an alternative to soil fumigation to control soil pathogens and protect soil health.

1. Introduction

Yam (Dioscorea opposite Thunb) is the fourth largest tuber crop in the world and has a high economic value [1]. Yam is widely grown in China, mainly in Jiangsu, Anhui, Hebei, and Henan provinces [2]. According to statistics, China’s annual production of yam has exceeded 10 million tons in 2020, ranking first in the world, which has a significant impact on global economic development [3]. Yam has a high nutritional value containing protein, polysaccharides, etc., and many secondary metabolites with beneficial effects on human health [4]. Yams are not commonly cultivated, because they are suitable for growing in loose and well-drained soil. The most suitable type of soil is the sandy soil or the sandy loam, with good water permeability and poor water retention, which is conducive to the growth and respiration of yam roots. Studies have shown that yam has effects such as delaying aging, lowering blood pressure, providing antioxidants, preventing cancer, and regulating immune function [5,6]. In recent years, with the improvement of people’s economic level in China, the medicinal health care purposes of yam have also received extensive attention [7]. The huge market demand has led to a rapid increase in the cultivation area of yam, but limited land resources have resulted in the continuous cultivation of yam [8]. Continuous cropping leads to an increase in soil pathogens, a decrease in soil fertility, and deterioration of the soil microbiological environment, which in turn leads to a reduction in yam production or even crop failures [9,10].
Soil fumigation is considered to be the most effective measure to address crop continuous cropping obstacles [11]. Fumigants such as chloropicrin, metham sodium, and dazomet have been widely used in vegetables, fruit trees, and ornamentals, and have successfully solved the problem of crop continuous cropping and increased the economic income of local farmers [9]. Chloropicrin is the most widely used fumigant in the market and has a good killing effect on soil pathogens and insects [12]. Li et al. [13] showed that chloropicrin fumigation had 93.60% and 82.57% control effects on Fusarium spp. and Phytophthora spp. in continuous strawberry soils at the picking stage, respectively. In addition, chloropicrin fumigation could effectively control the yam “paste” disease, which has increased the yam yield by 71% and the commercial rate by 81% [14]. However, the broad spectrum of chloropicrin also kills beneficial microorganisms in the soil [11]. Moreover, chloropicrin has a strong irritation and toxicity, which can cause respiratory difficulties, vomiting, headache, and other symptoms after absorption by the human body, and damage human health [15]. Therefore, there is an urgent need for control methods that can protect soil health while addressing the obstacles of crop continuous cropping.
Substrate cultivation is a soilless cultivation model in which plants grow in a solid substrate and absorb nutrients through the substrate to maintain normal growth and development [16]. Substrate cultivation is an important method to prevent soil-borne diseases and achieve efficient cultivation in agricultural production [17]. Compared with conventional cultivation methods, substrate cultivation economizes energy, water, and fertilizer, and reduces the use of pesticides to protect soil health [18]. Substrates can be divided into organic and inorganic substrates according to their composition. The chemical composition of organic substrates is relatively complex, including coir, mushroom slag, and agricultural waste [19]. The chemical stability of inorganic substrates is higher, containing slag, vermiculite, and perlite [20]. The composition of substrates is the main factor affecting the growth of plants in substrate cultivation, and the selection of a suitable cultivation substrate is an important way to ensure the green growth of plants.
Vermiculite is the second most widely distributed mineral in China and is inexpensive [21]. In addition, vermiculite has strong water and fertilizer retention properties, which can improve the soil aggregate structure and fertility [22]. Previous studies have shown that vermiculite has a high ion exchange capacity, which can release nutrients appropriately for plant absorption and utilization [23,24]. At present, most studies focus on the effects of vermiculite combined with other substrates on plant growth, and there is little attention on the effects of vermiculite on soil-borne diseases and plant growth when used alone in substrate cultivation. The effect of vermiculite on crop continuous cropping obstacles still needs to be further explored.
Hebei Province is the birthplace and important cultivation area of yam, among which “Xiaobaizui” yam is one of the famous types of yam and is welcomed by people for its high nutritional value and dense taste [25]. The region has a temperate climate with four distinct seasons, which is very suitable for the growth of yams. In addition, the soil in the region is sandy, loose, and fertile with plenty of moisture, and the unique soil structure leads to the unique and excellent quality of yams. In this study, we used chloropicrin fumigation as an experimental control to determine the effect of substrate cultivation on continuous cropping obstacles and yam growth through a 2-year field experiment. The effects of chloropicrin fumigation and substrate cultivation on soil nutrients, soil pathogens, soil microbial communities, and yam growth were investigated. We hypothesized that the planting model of vermiculite for substrate cultivation could replace chloropicrin fumigation and achieve the effects of promoting yam growth, protecting soil health, and reducing pesticide use. The objective of our study was to determine whether substrate cultivation could replace chloropicrin fumigation to control soil pathogens and increase yam yield.

2. Materials and Methods

2.1. Experimental Sites and Experimental Design

The experiment was conducted in Qingyuan District, Baoding City, Hebei Province, China in 2022 (38°75′ N, 115°49′ E). The average annual temperature, average annual precipitation, and average annual sunshine in this area were 12 °C, 451 mm, and 2700 h, respectively, which indicate a temperate monsoon climate. The experimental plot has been continuously planted with yam for a long time, and there are serious continuous cropping obstacles, and the yam planted in 2021 has already caused economic losses. The yam variety for the experiment was “Xiaobaizui”. The soil pH of the experimental plot was 8.72, the organic matter was 10.12 g/kg, and the contents of inorganic nitrogen, available phosphorus, and available potassium were 15.31, 25.89, and 155.46 mg/kg, respectively. The soil type was sandy loam.
A total of three treatments were set up in a randomized block group design for the field experiment: (1) CK: blank control without any treatment; (2) Pic: chloropicrin fumigation, chloropicrin (Dalian Lvfeng Chemical Co Ltd., Dalian, China, 99.5% purity) was uniformly applied to the soil at a dose of 50 g/m2, immediately covered with polyethylene film (Shandong Longxing Science and Technology Co Ltd., Weifang, China) for 20 d, and then the polyethylene film was removed for 20 d before planting yams; (3) SC: substrate cultivation, we first drilled apertures about 6 cm in diameter and 120 cm deep vertically using a mechanical drill bit (Figure 1A,B), then added 1 kg of vermiculite (2 mm, Hebei Green Life Agricultural Technology Co Ltd., Shijiazhuang, China) to each aperture (Figure 1C), and finally planted yams. Each treatment was replicated four times with a plot area of 30 m2. After all the treatments were completed, the yams were planted at the same time. The experiment was conducted for 2 years, and the treatments and field management were consistent each year. Yams were planted on 24 April 2022 and 18 April 2023 and harvested on 1 November 2022 and 28 October 2023, respectively.
It is worth noting that this substrate cultivation technology was different from conventional substrate cultivation as it was detached from the field environment. Most of the roots of yam were entangled in the loose space of the substrate, and the fibrous roots were still in contact with the surrounding field soil. The technology has been applied in Hebei province for a total of 133.4 hectares, successfully achieving the continuous planting of yam, and it has been proven to be suitable for clay soils as well. Our logic in considering SC was to replace part of the soil with vermiculite and study the effects of SC on soil pathogens and yam growth. It was also explored whether SC could reduce the negative effects on soil-beneficial microorganisms compared with chloropicrin fumigation.

2.2. Soil Samples

Rhizosphere soil samples were collected during yam harvest in 2022 and 2023 using the “shaking root method” [26], and five soil samples were randomly collected and mixed evenly in each plot according to the five-point sampling method. The fresh samples were sieved (2 mm) and divided into three parts: the first part was stored at 4 °C to determine the soil inorganic nitrogen content and the number of soil pathogens, the second part was air-dried to determine the soil pH and nutrients, the third part was stored at −80 °C for DNA extraction.

2.3. Soil pH and Nutrient Contents

Soil pH and nutrient contents were determined by referring to our previous method [9]. Briefly, soil pH was measured using a pH meter (Shanghai Leici Instrumentation, Shanghai, China). Soil organic matter content (SOM) was determined using the potassium dichromate external heating method at 175 °C. Soil ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N) were measured using a flow analyzer (Alliance Instruments, Eragny Sur-Oise, France). Soil available potassium (AK) and available phosphorus (AP) contents were measured using an FP640 flame photometer (Shanghai INESA Analytical Instrument Co., Ltd., Shanghai, China) and UV spectrophotometer (UV-2600, Shimadzu, Kyoto, Japan), respectively.

2.4. Soil Pathogens

The isolation and culture of soil pathogens referred to our previous method [13], which was simply as follows: 5 g soil sample was added to 95 mL distilled water, shaken for 30 min, and 1 mL of soil suspension was added to the culture medium of Fusarium spp. and Phytophthora spp., respectively. Then the soil suspension was put into three petri dishes and incubated at 28 °C for 3 days.

2.5. Yam Growth and Yield

According to the method of Silva et al. [27], at the time of harvest, 20 healthy yam plants were randomly selected from each plot and the length and diameter were measured with a straightedge. The fresh weight of each plant was also counted and recorded as the yield of yam. The number of diseased plants was investigated in each plot and the rate of diseased plants was counted, with the investigation method of the whole plot survey. Diseased plant rate = number of diseased plants/total number of investigated plants × 100%.

2.6. Soil Bacterial Community Analysis

According to the manufacturer’s instructions, soil DNA from the CK, Pic, and SC treatments was extracted from 0.25 g of soil using Powersoil® DNA Extraction Kit (Mo Bio, Laboratories Inc., Carlsbad, CA, USA) for a total of 12 samples. The extracted DNA samples were detected by 1% agarose gel electrophoresis, and then amplified by PCR using upstream primer 338F (5‘-ACTCCTACGGGGAGGCAGCAG-3′) and downstream primer 806R (5′-GGACTACHVGGGTWTCTAAT-3′) [13]. The PCR amplification procedures were as follows: firstly, predenaturation was performed for 3 min (95 °C); followed by 27 cycles of amplification, i.e., denaturation for 30 s (95 °C), annealing for 30 s (55 °C), and extension for 30 s, then stable extension for 10 min (72 °C) and finally storage at 4 °C. The amplified PCR products were recovered and purified for quantification using Qubit 4.0 (Thermo Fisher Scientific, Waltham, MA, USA), and then subjected to high-throughput sequencing on the Illumina PE 250 platform. Sequencing raw data were spliced by FLASH software (v 1.2.11, Adobe Systems Incorporated, San Jose, CA, USA) and processed by DADA2 plug-in noise reduction to obtain optimized sequences for analysis.

2.7. Data Analysis

One-way analysis of variance (ANOVA) was carried out using SPSS (V 20.0, IBM Corp., Armonk, NY, USA) to analyze the soil physical and chemical properties, the number of soil pathogens, and yam growth indexes. Data were expressed as mean ± standard deviation. The graphs were drawn using Origin 2022 software (OriginLab, Northampton, MA, USA). Differences in soil alpha diversity between treatments were analyzed using the Wilcoxon rank-sum test, and PCoA was analyzed based on the Bray–Curtis distance algorithm to test for differences in microbial composition between treatments. Wilcoxon rank-sum test was used to analyze species information with significant differences between treatments. Linear discriminant analysis (LDA) histograms were used to identify bacterial taxa with significant differences. LDA analysis was used to measure the magnitude of a species’ contribution to the differential effect, suggesting that the species may play a key role in the process of environmental change. This analysis could also be used as a way to find biomarkers in control and treatment groups. Spearman correlation coefficient was used to evaluate soil microorganisms at the genus level with environmental factors. Correlations among soil physical and chemical properties, soil pathogens, and yam growth were analyzed based on the person correlation.

3. Results

3.1. Changes in Soil pH and Nutrients

Pic and SC treatments significantly reduced soil pH by 2.04–3.55% and 2.64–3.78% compared with CK, respectively (Table 1). The contents of soil SOM, NH4+-N, and NO3−-N in the Pic and SC treatments were significantly higher than those in the CK treatment. The changes in soil AK in 2022 were similar to pH, with Pic and SC treatments significantly reducing AK content by 29.29% and 4.04%, respectively. However, the AK content under SC treatment in 2023 was the highest. Soil AP varied differently. SC treatment had the highest soil AP content, while the Pic treatment had significantly lower AP content than CK. The soil AK and AP contents after Pic treatment were the lowest in the two years of experiments. Soil SOM, NH4+-N, AK, and AP contents all increased under SC treatment compared to Pic, while NO3−-N content was significantly decreased. There were no significant differences in soil pH between Pic and SC treatments. The contents of soil pH, SOM, AK, and AP in each treatment showed a decreasing trend in 2023.

3.2. Changes in Soil Pathogens

Pic and SC treatments significantly reduced the number of soil pathogens compared to CK (Figure 2, Table S1). Fusarium spp. and Phytophthora spp. were significantly decreased by 73.89–88.22% and 66.74–85.91% under Pic and SC treatments, respectively. Moreover, Pic treatment had the lowest number of Fusarium spp. and Phytophthora spp., which were significantly lower than CK and SC treatments. This indicated that Pic was the most effective against soil pathogens.

3.3. Changes in Growth Indicators and Yield of Yam

The resulting yam of each treatment at the harvest time is shown in Figure S1. Yam yield after Pic and SC treatments significantly increased by 73.60–89.55% and 56.87–73.43% compared with CK, respectively (Figure 3A, Table S2). In addition, yam yield after the Pic treatment was significantly increased by 10.66% and 9.29% compared with SC treatment in 2022 and 2023, respectively. The rate of diseased plants was significantly lower for both the Pic and SC treatments than for CK, and there was no significant difference between the two treatments (Figure 3B). The yam length after the SC treatment was the highest, which increased by 148.59–175.71% and 19.37–23.19% compared with the CK and Pic treatments, respectively (Figure 3C). The changes in yam diameter were opposite to the changes in plant length, with SC treatment producing the lowest yam diameter, which was reduced by 20.22–26.54% and 8.84–11.77% compared with the CK and Pic treatments, respectively (Figure 3D).

3.4. Changes in Soil Bacterial Community

3.4.1. Alpha Diversity

Pic and SC treatments significantly reduced the Shannon, Chao1, and ACE indexes of the soil bacterial community (Table 2), indicating that soil fumigation and substrate cultivation reduced the diversity and abundance of the soil bacterial community. The Pic treatment had the lowest Shannon, Chao1, and ACE indexes, indicating that the Pic treatment had the greatest effect on the alpha diversity of the bacterial community. A higher Simpson index indicated lower microbial diversity. The Simpson index after the Pic treatment was the highest, indicating that Pic significantly reduced the diversity of the soil bacterial community, which corresponded to the change in the Shannon index.

3.4.2. Venn Diagram and Beta Diversity

Compared with CK, the number of unique OTUs in the bacterial community decreased after the Pic and SC treatments (Figure 4A,B). The SC treatment had an 8.07% more unique OTU than the Pic treatment in 2022, while it was 27.71% less than the Pic treatment in 2023. Moreover, the unique OTU differences among the three treatments were smaller in 2023 than in 2022, and the number of shared OTUs was higher. PCoA analysis showed that the Pic, CK, and SC treatments were in different quadrants, indicating that the Pic and SC treatments significantly changed the soil bacterial community (Figure 4C,D). The total degree of explanation of PCoA for the differences in soil bacterial community structure in 2022 and 2023 was 80.29% and 61.07%, respectively.

3.4.3. Species Composition

We analyzed the differential species of the soil bacterial community among the treatments. Actinobacteriota, Proteobacteria, Acidobacteriota, and Chloroflexi were the dominant bacterial phyla in the soil (Figure 5A,C). Compared with CK, Pic treatment significantly decreased the abundance of Actinobacteriota, Acidobacteriota, and Chloroflexi, while increasing the abundance of Proteobacteria. SC treatment significantly increased the abundance of Actinobacteriota and Acidobacteriota, while decreasing the abundance of Chloroflexi. Compared with CK, the relative abundance of Proteobacteria treated by SC decreased in 2022 but increased in 2023. In addition, SC treatment significantly increased the abundance of Actinobacteriota, Acidobacteriota, and Chloroflexi compared with Pic treatment. At the genus level, Pic and SC treatments significantly increased the abundance of Bacillus, Paenibacillus, Paenisporosarcina and decreased the abundance of Nitrospira compared with CK (Figure 5B,D). Bacillus was the most abundant and Nitrospira was the least abundant in the Pic treatment compared with CK and SC treatments. SC treatment also significantly increased the abundance of Gaiella, RB41, and Nitrospira compared with Pic treatment.

3.4.4. Biomarkers Analysis

The LDA discriminant plot shows that a total of 37 and 39 biomarkers were screened under all treatments in 2022 and 2023, respectively (Figure 6). We screened 18, 12, and 7 biomarkers in CK, Pic, and SC treatments in 2022, and 14, 19, and 6 biomarkers in CK, Pic, and SC treatments in 2023, respectively. At the genus level, LDA analysis screened 5 biomarkers for the bacterial community in 2022 (4, 1, and 0 for CK, Pic, and SC, respectively) and 9 biomarkers for the bacterial community in 2023 (3, 4, and 2 for CK, Pic, and SC, respectively). In addition, CK was mainly enriched for Pseudarthrobacter, Pic was enriched for Bacillus. The results showed that the response of bacterial community to Pic treatment was higher than that to SC treatment.

3.4.5. Correlation between Soil Microorganisms, Environmental Factors and Yam Growth

We analyzed the correlations between the top 30 bacterial genera and environmental factors (Figure 7). The results showed that there were strong correlations between bacterial genera and soil physicochemical properties, the number of soil pathogens, and yam yield. Significant positive correlations were found between yam yield and Bacillus, Paenibacillus, Micromonospora, and Streptomyces, and significant negative correlations were found with MND1 and Nitrospira. Soil pathogens showed a significant positive correlation with Pseudarthrobacter, MND1, and Nitrospira and a negative correlation with Bacillus, Paenibacillus, and Micromonospora. Bacillus was significantly positively correlated with NO3−-N and negatively correlated with AP and diseased plant rate. Pseudarthrobacter showed a significant positive correlation with AK and AP and a negative correlation with NO3−-N. Nitrospira was significantly positively correlated with AP and diseased plant rate and negatively correlated with NO3−-N.

3.5. Correlation Analysis of Yam Plant Growth and Soil Environmental Factors

Person correlation analysis showed that yam yield was significantly and positively correlated with SOM, NH4+-N, NO3−-N, and AK and negatively correlated with pH, Fusarium spp., Phytophora spp., and diseased plant rate (Figure 8). Soil pathogens showed a significant positive correlation with pH, diseased plant rate, and diameter and a negative correlation with SOM, NH4+-N, NO3−-N, and AK. In addition, the correlation analysis of diseased plant rate and yield showed opposite results, and when one was positively correlated with environmental factors, the other was negatively correlated with environmental factors. The correlation between yam length and environmental factors was similar to that of yam yield, both of which were significantly negatively correlated with yam diameter.

4. Discussion

4.1. Effects of Soil Fumigation and Substrate Cultivation on Soil pH and Nutrients

Soil pH is a key factor influencing soil nutrient uptake, utilization, and cycling processes [28]. We found that Pic treatment significantly reduced soil pH, which is consistent with Wang et al. [29]. SC treatment also significantly reduced soil pH, probably due to the cation exchange property of vermiculite, which exchanged with H+ and reduced soil pH [23]. SOM is considered to be an important source of plant nutrients, which is positively correlated with soil nutrient levels in a certain range [9]. Ou et al. [30] showed that chloropicrin fumigation increased SOM, which was confirmed by our results. However, Yang et al. [31] reported that chloropicrin fumigation decreased SOM, and this difference may be due to the difference in soil types, leading to opposite results. Vermiculite is rich in mineral elements and adsorbs organic matter from fertilizers, releasing it slowly for plant uptake and utilization [24], which may be the reason why SC treatment significantly increased SOM.
In addition, we found that Pic and SC treatments increased soil NH4+-N and NO3−-N. Chloropicrin fumigation can kill some soil microorganisms and convert organic nitrogen into inorganic nitrogen in soil microorganisms, thus increasing the content of inorganic nitrogen in the soil [32]. Moreover, vermiculite has a strong water and fertilizer retention capacity, which can accommodate more nitrogen fertilizer for crop uptake and utilization [33]. We found that yam growth was better under Pic and SC treatments compared with CK, indicating that yam would absorb more nutrients including potassium, resulting in less potassium remaining in the soil. This may be one of the reasons why Pic and SC reduced available potassium in 2022. Soil AK content of SC treatment in 2023 was the highest, which may be related to the adsorption capacity of vermiculite. Li et al. [34] showed that chloropicrin fumigation reduced soil available phosphorus, which is consistent with our results. In contrast, SC treatment increased the available phosphorus content, which may be related to the adsorption capacity of vermiculite.

4.2. Effects of Soil Fumigation and Substrate Cultivation on Soil Pathogens

The efficacy of chloropicrin fumigation against soil pathogens has been reported previously [13,14,35]. There are few reports on the use of vermiculite for substrate cultivation against soil pathogens. He et al. [36] showed that the antibacterial rate of modified vermiculite against Escherichia coli and Staphylococcus aureus reached 94.0% and 99.9%, respectively. Wang et al. [37] reported that vermiculite mixed with charcoal and vinegar residue could significantly reduce the disease index of cucumber Fusarium wilt, and the inhibitory effect of vermiculite:charcoal:vinegar residue = 1:1:3 was the best. We found that Pic and SC treatments effectively reduced the number of Fusarium spp. and Phytophthora spp, indicating that SC had effects similar to Pic in controlling soil pathogens. Pic had the best control effect on soil pathogens, which may be related to the residual effects of chloropicrin or differences in microbial community dynamics [38]. Correlation analysis showed that soil pathogens and pH were significantly positively related, indicating that low pH could control the reproduction and spread of soil pathogens.

4.3. Effects of Soil Fumigation and Substrate Cultivation on Yam Growth

Previous studies have shown that chloropicrin fumigation promoted plant growth and significantly increased crop yield [14,39]. In the present study, we observed that chloropicrin fumigation had the highest yam yield and significantly increased yam length. In addition, SC treatment also significantly promoted yam growth, increased yam yield, and reduced the rate of diseased yam plants. Liu [40] showed that vermiculite used in substrate cultivation significantly increased plant height, stem thickness, root length, root-shoot ratio, and the fresh weight of peppers. Sun et al. [41] reported that a vermiculite:sphagnum mixture at a ratio of 2:1 significantly increased blueberry yield, plant height, and diameter as well as improving the blueberry quality. In addition, substrate cultivation could shorten the time of cultivation and increase the protein and flavor of oyster mushrooms [42]. Correlation analysis showed a significant negative correlation between yam yield and soil pathogens, indicating that the propagation of soil pathogens would inhibit yam growth. Yam yield was positively correlated with SOM and inorganic nitrogen content. SOM represents the fertility status of the soil, and generally, soils with higher SOM content produce higher crop yields [43]. We found that Pic and SC treatments significantly reduced the diameter of yam, which may be related to the fact that yam is more likely to grow vertically in a healthy soil environment. In our study, the yam yield of SC treatment was lower than that of Pic treatment but significantly higher than that of the control, which could be an effective alternative model for chloropicrin fumigation.

4.4. Effects of Soil Fumigation and Substrate Cultivation on Soil Bacterial Community

Soil microorganisms are the most valuable biological resources in ecosystems and play an irreplaceable role in maintaining soil health [44]. Some microorganisms can decompose organic matter in soil and participate in soil nutrient cycling, which is closely related to plant growth [45]. We found that Pic and SC treatments reduced the diversity (Shannon and Simpson index) and richness (Chao1 and ACE index) of the bacterial community in soil, and Pic had the greatest effect on the bacterial community. Soil fumigation could kill most microorganisms in the soil, thus reducing the diversity and richness of the bacterial community [46]. This may partially explain the reduction of soil diversity and richness by Pic. As an inorganic substrate, vermiculite does not contain microorganisms and organic matter [47], and therefore has low microbial diversity. PCoA analysis showed that the microbial community was significantly altered by Pic treatment, which was the main factor responsible for the differences among treatments. In this study, the abundance of Actinobacteriota and Acidobacteriota decreased under Pic treatment and increased under SC treatment. Actinobacteriota are usually found in soils with high organic matter and can effectively inhibit the propagation and spread of soil pathogens [48]. Xu et al. [49] reported that Acidobacteriota is an important microorganism that drives soil material cycling and maintains soil homeostasis. The SC treatment had the highest SOM content and was more environmentally friendly compared with the Pic treatment, thus SC significantly increasing the abundance of Actinobacteriota and Acidobacteriota. Proteobacteria has been reported to be the largest bacterial phylum in soil and plays an important role in nutrient supply [50]. Pic increased the abundance of Proteobacteria, contrary to Zhang et al. [51], which may be due to the complex interactions between different soils and plants. The abundance of Proteobacteria treated by SC decreased in 2022 and increased in 2023, which was consistent with Li et al. [52].
Lyng and Kovács [53] reported that Bacillus is a plant-promoting bacterium that can improve soil fertility and promote crop growth. The highest abundance of Bacillus was found in Pic, which may also be one of the reasons for the significant increase in yam yield under Pic treatment. Correlation analysis showed that the abundance of Bacillus was significantly positively correlated with yam yield and negatively correlated with soil pathogens. Soil nitrification driven by Nitrospira plays a key role in nitrogen cycling [54,55]. Nitrospira was significantly increased by the SC treatment compared with Pic, which indicates that SC has a positive role in promoting soil nitrogen cycling. The microbial diversity of the SC treatment was significantly higher than that of the Pic treatment and had the fewest biomarkers, indicating that SC had less impact on the soil microcosmic environment.

5. Conclusions

We investigated the effects of chloropicrin fumigation and substrate cultivation on yam growth, soil pathogen control, soil physicochemical properties, and soil microbial communities. The results showed that both chloropicrin fumigation and substrate cultivation could effectively control soil pathogens, reduce the disease rate of yam plants, and significantly increase yam yield. Correlation analysis showed that yam growth was significantly negatively correlated with soil pathogens. In addition, soil organic matter, available phosphorus, and available potassium were higher in substrate cultivation, significantly higher than those in chloropicrin fumigation. Some soil-beneficial microorganisms such as Actinobacteriota, Acidobacteriota, and Bacillus were significantly increased in substrate cultivation. Notably, substrate cultivation had less impact on the soil microecological environment compared with chloropicrin fumigation. In conclusion, substrate cultivation could be an effective alternative model to chloropicrin fumigation for controlling soil pathogens and promoting plant growth. Substrate cultivation not only reduced pesticide use, but also protected soil health.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agriculture14081231/s1, Figure S1: Each treatment of yams at harvest time; Table S1: Changes in soil pathogens; Table S2: Changes in growth indicators and yield of yam.

Author Contributions

Conceptualization, X.J.; methodology, Z.H.; software, Y.S.; validation, L.G.; formal analysis, F.H.; investigation, X.J.; resources, Y.S.; writing—original draft preparation, Q.L.; writing—review and editing, A.C. and Q.L.; project administration and funding acquisition, A.C. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key Research and Development Program of China, grant number 2023YFD1701205.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

All data are contained within the manuscript.

Acknowledgments

We thank Wenbiao Liu for his help with this research.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. The process of substrate cultivation (SC) treatment ((A): drilling apertures with a mechanical drill bit, (B): the shape of the apertures, (C): vermiculite addition).
Figure 1. The process of substrate cultivation (SC) treatment ((A): drilling apertures with a mechanical drill bit, (B): the shape of the apertures, (C): vermiculite addition).
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Figure 2. Changes in soil Fusarium spp. (A) and Phytophthora spp. (B) under different treatments. Values are mean ± standard error, different letters indicate significant differences (p < 0.05).
Figure 2. Changes in soil Fusarium spp. (A) and Phytophthora spp. (B) under different treatments. Values are mean ± standard error, different letters indicate significant differences (p < 0.05).
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Figure 3. Changes in yam yield (A), diseased plant rate (B), length (C), and diameter (D) under different treatments. Values are mean ± standard error, different letters indicate significant differences (p < 0.05).
Figure 3. Changes in yam yield (A), diseased plant rate (B), length (C), and diameter (D) under different treatments. Values are mean ± standard error, different letters indicate significant differences (p < 0.05).
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Figure 4. Venn diagram (A,B) and PCoA analysis (C,D) of soil bacterial community.
Figure 4. Venn diagram (A,B) and PCoA analysis (C,D) of soil bacterial community.
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Figure 5. Differences in soil microbial abundance at phylum level (A,C) and genus level (B,D). The number of asterisks indicates significance: * p < 0.05, ** p < 0.01.
Figure 5. Differences in soil microbial abundance at phylum level (A,C) and genus level (B,D). The number of asterisks indicates significance: * p < 0.05, ** p < 0.01.
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Figure 6. Biomarker analysis of bacterial communities in 2022 (A) and 2023 (B).
Figure 6. Biomarker analysis of bacterial communities in 2022 (A) and 2023 (B).
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Figure 7. Correlation between soil microorganisms, environmental factors, and yam growth in 2022 (A) and 2023 (B). The number of asterisks indicates significance: * p < 0.05, ** p < 0.01, *** p < 0.001.
Figure 7. Correlation between soil microorganisms, environmental factors, and yam growth in 2022 (A) and 2023 (B). The number of asterisks indicates significance: * p < 0.05, ** p < 0.01, *** p < 0.001.
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Figure 8. Correlation analysis between yam plant growth and soil environmental factors. DPR: Diseased plant rate. The number of asterisks indicates significance: * p < 0.05, ** p < 0.01, *** p < 0.001.
Figure 8. Correlation analysis between yam plant growth and soil environmental factors. DPR: Diseased plant rate. The number of asterisks indicates significance: * p < 0.05, ** p < 0.01, *** p < 0.001.
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Table 1. Soil pH and nutrients under different treatments.
Table 1. Soil pH and nutrients under different treatments.
YearTreatmentpHSOM (g/kg)NH4+-N
(mg/kg)		NO3−-N
(mg/kg)		AK
(mg/kg)		AP
(mg/kg)
2022CK8.73 a10.10 c2.91 b12.46 c157.37 a26.13 b
Pic8.42 b12.38 b3.10 a16.96 a111.28 c21.25 c
SC8.40 b13.50 a3.25 a14.53 b151.02 b50.50 a
2023CK8.34 a9.67 b3.24 c13.04 c125.70 b25.17 b
Pic8.17 b12.13 a3.46 b16.47 a108.16 c21.67 c
SC8.12 b12.27 a3.63 a14.89 b136.28 a49.40 a
Different letters for the same indicator indicate significant differences among treatments (p < 0.05).
Table 2. Alpha diversity under different treatments.
Table 2. Alpha diversity under different treatments.
YearTreatmentShannonSimpsonChao1ACE
2022CK7.35 a0.0030 b8924.4 a10012.4 a
Pic6.45 c0.0064 a5121.8 c5336.0 c
SC7.19 b0.0035 b7238.3 b7423.5 b
2023CK7.38 a0.0017 b7964.0 a7971.1 a
Pic7.04 c0.0026 a5380.6 c5473.2 c
SC7.28 b0.0025 a7346.7 b7408.2 b
Different letters for the same indicator indicate significant differences among treatments (p < 0.05).
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Jin, X.; Hao, Z.; Song, Y.; Gao, L.; He, F.; Li, Q.; Cao, A. Response of Yam Yield and Soil Microbial Communities to Soil Fumigation and Substrate Cultivation. Agriculture 2024, 14, 1231. https://doi.org/10.3390/agriculture14081231

AMA Style

Jin X, Hao Z, Song Y, Gao L, He F, Li Q, Cao A. Response of Yam Yield and Soil Microbial Communities to Soil Fumigation and Substrate Cultivation. Agriculture. 2024; 14(8):1231. https://doi.org/10.3390/agriculture14081231

Chicago/Turabian Style

Jin, Xi, Zheng Hao, Yelong Song, Lan Gao, Fuqiang He, Qingjie Li, and Aocheng Cao. 2024. "Response of Yam Yield and Soil Microbial Communities to Soil Fumigation and Substrate Cultivation" Agriculture 14, no. 8: 1231. https://doi.org/10.3390/agriculture14081231

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