Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil’s nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil’s NH4+-N, NO3−-N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil’s temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil’s bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.

Chloropicrin (CP) controls soil-borne plant diseases caused by pathogenic microbes, increases crop yield, but has a long-term inhibitory effect on beneficial soil microorganisms. Therefore, we evaluated the effects of biofumigation material fresh chicken manure (FCM) on soil microorganisms, and the duration of those effects in this experiment. Our results showed that in the laboratory, FCM significantly increased substrate-induced respiration (SIR) of soil microorganisms by 2.2–3.2 times at 80 d compared to the control, however, CP significantly inhibited the SIR of soil microorganisms. FCM and CP increased NH4+-N concentration within 40 days which then returned to the control level. FCM increased NO3--N by 2.82–5.78 times by 80 days, compared with the control, while the concentration of NO3--N in the CP treatment was not significantly different from the control at the 80 day. Although in the laboratory FCM inhibited the relative abundance of 16 S rRNA and the nitrogen cycle functional genes AOA amoA, AOB amoA, nirK and nosZ over a 40-day period, the taxonomic diversity of soil bacteria and fungi in the FCM treatment were restored to unfumigated level within 90 days in the field. However, CP treatment has a strong inhibitory effect on soil microorganisms after 90 days. Importantly, the relative abundance of some beneficial microorganisms that control soil-borne pathogenic microbes or degrade pollutants increased significantly in FCM, including Bacillus, Pseudomonas and Streptomyces bacterial genera and Chaetomium and Mycothermus fungal genera. Noteworthy, like CP, FCM still had a strong inhibitory effect on Fusarium at 90 d. Our results indicated that FCM not only increased the content of inorganic nitrogen and improved the respiration rate of soil microorganisms, but it also shortened the recovery time of beneficial soil microorganisms and increased taxonomic diversity. Our previous reports showed that FCM and CP treatments had the same effect in disease control and crop growth. Combined with the results of this experiment, we believe that FCM has the potential to replace CP, which would eliminate CP's detrimental environmental impact, improve farmer safety and promote sustainable crop production.

Sugarcane cultivars (Saccharum officinarum L.) are widely cultivated for both sugar and renewable energy in China. The response of rhizosphere fungal composition and diversity to different emerging sugarcane cultivars is limited. Therefore, utilizing high-throughput sequencing, we explored fungal communities’ structure in soils adhering to six sugarcane cultivars’ roots (Guitang 08–120, Regan14-62, Guitang 08–1180, Haizhe 22, Liucheng 05–136, Taitang 22) in Guangxi Province, China. Our results suggested that sugarcane varieties significantly altered rhizosphere soil attributes, with Haizhe 22 having substantially lower soil pH, organic matter (OM), available phosphorus (AP), and soil water contents (SWC) than others cultivars. Different sugarcane varieties did not substantially affected the Shannon fungal diversity index, but the apparent effect on fungal richness was significant. Beta diversity analysis revealed that “Haizhe 22” distinguished the fungal community from the other five cultivars. Soil pH, OM, cultivars, and soil moisture were crucial determinants in shaping soil fungal composition. The Haizhe 22 rhizosphere significantly enriched the operational taxonomic units (OTUs) assigned to two fungal genera (Cephalotheca and Sagenomella), while rhizosphere of other verities significantly enriched the OTUs assigned to four fungal genera (Chaetomium, Chaetosphaeria, Mortierella, and Talaromyces), suggesting their essential role in plant development, disease tolerance, and bioremediation. These findings may help in selecting or breeding innovative genotypes capable of supporting abundant rhizosphere fungi beneficial to plants that would likely improve crops’ agronomic potential and maintain soil ecosystem sustainability.

Composting has been a rational method to dispose of horse or wildlife animal manures, especially in the developed cities with horse clubs and wildlife parks. However, few studies have focused on the mechanism and improvement methods for composting the horse or wildlife animal manures. In this study, we investigated the effect of exogenous compound enzymes on thermophilic composting, which could potentially support the management of horse and wildlife animal manures. With the presence of exogenous enzymes, the duration of high temperature (> 60 °C) was significantly prolonged (p < 0.05), and the germination index was significantly improved (p < 0.05). More-efficient improvement of composting maturity was associated with the addition of that exogenous enzyme that might influence microflora succession and the interaction among microorganic communities, especially fungal, during the composting process. Furthermore, redundancy and canonical correspondence analyses indicated that the C/N ratio, temperature, and germination index were significant variations to influence bacterial communities (p < 0.05). The dominant Flavobacterium, Thermopolyspora, Thermomonospora, and Chaetomium and Saccobolus could play an essential role in carbohydrate and phytotoxin degradation, while Thermobispora and norank_f_Limnochordaceae could lead to temperature rising.