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.

Animal manure application to soils is considered to be one of the main cause of antibiotic and bacterial pathogen spread in the environment. Pig livestock, which is the source of one of the most used fertilizer for cultivated land, is also a hotspot for antibiotics and antibiotic-resistant bacteria. Besides harsh chemical and physical sanitization treatments for the abatement of antibiotics and bacterial load in livestock waste, more sustainable and environmentally friendly strategies need to be considered. In this context, the use of natural substances which are proved useful for pest and disease control is currently under exploration for their role in the reduction of bacterial pathogen population. Among these, plants and derived products from the Brassicaceae family, characterized by the presence of a defensive glucosinolate-myrosinase enzymatic system, have been successfully exploited for years in agriculture using the so-called biofumigation technique against crop diseases. Although the application of biofumigation to suppress a range of soil borne pests has been well documented, no studies have been examined to reduce bacterial population in animal waste. In the present study, the release and the antibacterial activity of bioactive compounds deriving from different Brassicaceae defatted seed meals against pathogens and bacterial population in pig manure is addressed. Rapistrum rugosum and Brassica nigra defatted seed meals were found to be the most active products against tested pathogens and able to significantly reduce the bacterial load in the manure.

Plants of the order Brassicaceae have evolved a chemical defence against herbivory: the glucosinolate-myrosinase system. Mechanical damage to plant tissues, such as grazing, initiates the production of phenethyl isothiocyanate (PEITC), a compound toxic to invertebrates. Mechanical damage caused during biofumigation and the harvesting and washing of watercress presents routes for PEITC release into waterbodies, such as the chalk stream spawning sites of brown trout (Salmo trutta). This laboratory study exposed developing S. trutta embryos to PEITC at concentrations of 0.01, 0.1 and 1 μg/L. S. trutta exposed to 1 μg/L PEITC during embryonic development resulted in 100% mortality after four dose days. Exposure to 0.1 μg/L PEITC resulted in an approximate fourfold increase in mortality relative to the controls, while exposure to 0.01 μg/L PEITC had a negligible effect on embryo mortality. Embryos exposed to 0.1 μg/L PEITC showed a significant delay in hatching and produced alevins with significantly shorter total lengths, lighter body weights and an approximate threefold increase in spinal deformities relative to those exposed to the controls and 0.01 μg/L PEITC. The results of a motor activity assay demonstrate that alevins exposed to PEITC showed a significant decrease in swimming activity compared with control animals during periods of illumination. The increased mortality, teratogenic effects and impaired behaviour in S. trutta following embryonic exposure to relatively low concentrations of PEITC highlight a need to accurately quantify and monitor environmental levels of PEITC.

Biofumigation is considered a good alternative to chemical fumigation because it can control crop pathogens and diseases with lower health and environmental risks than chemical fumigants. Glucosinolates are volatile compounds found in most Brassica species, and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. However, the effect of glucosinolates and their breakdown products on non-target and beneficial soil organisms is not well documented. Three biofumigants, broccoli, mustard and oilseed radish, were evaluated for their effect on earthworms (Eisenia andrei) and the soil microbial community. Sub-lethal endpoints, including growth and reproductive success of the earthworms, were monitored. Genotoxicity of the biofumigants towards earthworms was evaluated by means of the comet assay. Broccoli reduced earthworm reproduction while mustard induced more DNA strand breaks in earthworm cells compared to the control. Soil microbial community function and structure were evaluated by means of community level physiological profiling and phospholipid fatty acid analyses. The effects exerted by the biofumigants on the microbial community were the most pronounced within the first 14 days after application. Carbon substrate utilisation was most affected by the oilseed radish treatment and microbial community structure by the mustard treatment.