Non-target Soil Microorganisms Research Articles

Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology.

Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts and a belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform the functions necessary for agricultural production, it is thus important to evaluate the performance of these systems through the lens of soil organisms, especially soil microbes. They provide numerous services to plants, including growth promotion, nutrient supply, tolerance to environmental stresses and protection against pathogens. An overwhelming majority of studies confirm that ecology-based agricultures are beneficial for soil microorganisms. However, three practices were identified as posing potential ecotoxicological risks: the recycling of organic waste products, plastic mulching, and pest and disease management with biopesticides. The first two because they can be a source of contaminants; the third because of potential impacts on non-target microorganisms. Consequently, developing strategies to allow a safe recycling of the increasingly growing organic matter stocks produced in cities and factories, and the assessment of the ecotoxicological impact of biopesticides on non-target soil microorganisms, represent two challenges that ecology-based agricultural systems will have to face in the future.

Destruction of transgenic potato plants (Solanum tuberosum L.) remnants under the influence of soil microbiome

Scientific community has been considering various hypotheses regarding the possible impact of GM plants on non-target soil microorganisms for decades, distinguishing direct and indirect effects. Direct effects are usually easier to detect, as transgenic proteins, characterized by a range of elimination against certain types of insects, pathogenic fungi and bacteria, can affect non-target beneficial symbionts and soil microbial groups involved in the transformation of organic substances. Indirect effects are difficult to assess, as many different factors can affect the composition of root exudates and the metabolic activity of plants. Changes in metabolic pathways can affect the composition of soil exudates and gene expression in plant tissues. At the same time, these changes can affect the decomposition of organic matter and the course of microbiological processes in the soil. Based on experimental studies, an assessment of the rate of destruction of plant residues and DNA degradation in transgenic potato plants in soddy-podzolic soil of potato crop rotation was carried out. The results of the studies have established a significant role of the microbiome of soddy-podzolic soil of potato crop rotation in the destruction of residues of transgenic potato plants and DNA degradation. Destruction of residues of transgenic plants under the influence of microflora of soddy-podzolic soil of potato crop rotation was 30 days with a loss of raw mass 87.14±1.11%. DNA degradation over this period is 88% (186 ng/mg) from the initial amount of total DNA, and degradation of nptII and 35S genes — about 90% from their initial amount in PCR products. It was found that about 90% of nptII and 35S genes in DNA residues of transgenic potato plants under the influence of microbiome soddy-podzolic soil occurs on day 30.

IMPACT OF ATRAZINE AND BROMOXYNIL ON THE COLONY FORMING UNITS (CFU) OF SOIL BACTERIA

According to overwhelmingly positive effects throughout time, herbicide treatment has become a crucial component of thriving agricultural output worldwide. However, its detrimental effects on non-target soil microorganisms involved in the nitrogen cycle, nutrient degradation, and organic matter breakdown must be considered. In the current study, the consequences of the two (2) herbicides that are most often used in Pakistan, Atrazine and Bromoxynil, were evaluated on soil bacteria over the course of fifteen consecutive days (exposure period). Recommended field rate of herbicide application was followed (i.e. active ingredient of 6.17 mg for Atrazine and 2.4 mg for Bromoxynil per gm of soil). During the investigations half and double recommended doses of these herbicides were used. Time interval of 5, 10 and 15 days were used to determine the bacterial populations. Statistical analysis of the investigation revealed that the bacterial population did not exhibit any appreciable variations in relation to the exposure duration (p 0.05). The Atrazine application along with the herbicide treatments, reduced the bacterial population during all the tested interval durations with just half of the suggested field rate. The current study reflected that apart from the benefit of herbicides in controlling weeds these chemicals also effect bacterial population that is a serious issue for present and future agriculture. Further, the same study needs to be perform under field conditions to confirm the finding of laboratory results before issuing solid recommendations to the farming community.

Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng.

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported. We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment. The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng's survival rate and stimulated plant growth, ensuring P. notoginseng's healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins' niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria. In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Nanopesticide risk assessment based on microbiome profiling – Community structure and functional potential as biomarkers in captan@ZnO35–45 nm and captan@SiO220–30 nm treated orchard soil

Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35–45 nm or SiO220–30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220–30 nm as a nanocarrier speeds up a recovery process compared to ZnO35–45 nm.

Assessment of the ecotoxicological impact of captan@ZnO35–45nm and captan@SiO2 20–30nm nanopesticide on non-target soil microorganisms – A 100-day case study

Nanopesticide application should enable efficient pest management with smaller doses of an active ingredient. Nevertheless, the environmental risk assessment of nanopesticides is currently in its initial stages due to limited access to nanopesticides. Therefore, we synthesised nanofungicides with captan as an organic active ingredient and ZnO35–45nm or SiO2 20–30nm as nanocarriers (captan@ ZnO35–45nm and captan@ SiO2 20–30nm) and evaluated their environmental risk by testing different microbial parameters as its potential biomarkers. First, physicochemical analysis (SEM-EDS, XPS, and FTIR) confirmed the presence of captan in nanofungicides, and they maintained 43–61 % antifungal efficiency against pathogen fungi compared to captan. Second, a laboratory toxicity assay (spot test) showed that nanofungicides generally revealed 10–100-fold lower growth inhibition of non-target microbial strains compared to captan. Next, the effect of nanofungicides on the abundance, structure and function of non-target soil microorganisms was evaluated during the 100-day microcosm using orchard soil and compared to control, captan, and nanocarriers. The changes in the total number of bacteria, ammonia-oxidising bacteria (AOB) and fungi were enumerated using the copy number of the qPCR approach based on the copy number of 16S rRNA, amoA and ITS genes. The functional potential and microbial structure were estimated based on Community Level Physiological Profiles (CLPPs) and Phospholipid Fatty Acids (PLFAs) profiles. Generally, results indicated that nanofungicides affected soil microorganisms by changing, in different scale, various microbial parameters, but their negative effect was generally lower than pesticide. Although qPCR results revealed the harmful effect of all tested compounds on total bacteria number (16S rRNA) on day 42, and captan@ZnO35–45nm and nanocarrier SiO2 20–30nm still affected amoA gene copy number on day 100, but the total fungal abundance in orchard soil was not affected. Furthermore, the analyses of functional and structural microbial diversity indicated the recovery process that was the fastest for captan@SiO2 20–30nm nanofungicide. On the contrary, ZnO35–45nm increased and prolonged the negative effect of captan in synthesised nanofungicide and generally exerted a more profound and/or longer effect than SiO2 20–30nm nanocarrier. Therefore we conclude that SiO2 20–30nm has better potential to be used as a nanocarrier compared to ZnO35–45nm. More studies are needed but soil microorganisms as sensitive biomarkers should be used for environmental risk assessment of nanopesticides.

Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system

Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.

Effect of Atrazine, 2,4-D Amine, Glyphosate and Paraquat Herbicides on Soil Microbial Population

Herbicides’ toxic impact on the non-target soil microorganisms which play roles in degrading organic matter, nitrogen and nutrient recycling and decomposition needs to be considered. In the present study, the effect of four (4) most commonly used herbicides, viz; atrazine, 2, 4- D amine, glyphosate and paraquat on soil microorganisms was assessed over a period of fifteen continuous days (exposure period). The herbicide treatments were the normal recommended field rate, (6.67 mg active ingredient per gram of soil for atrazine, 6.17 mg for 2, 4-D amine, 5.56 mg for glyphosate, and 2.46 mg for paraquat), half and double of the recommended field rates. Tables 4.1 through 4.5 showed the various heterotrophic bacterial colony counts obtained from the various treatments, ranging from the control (Day 1; no herbicide applied) to days 3, 6, 9 and 15 after the application of the various herbicides, respectively. Two general trends are readily observed: the first is that, upon application of the herbicide, the microbial growth steadily diminishes, up to the 6th day. However, from there it continues to increase till the end of the experiments (day 15). This applies to each herbicide. Firstly, the effect of the addition of the various herbicides was evaluated using two samples, a two-tailed Z-Test for means, at a 95% confidence interval, and the results showed that there is a difference in the bacterial counts before the application of the herbicides (Day 0) and immediately after (day 3), and the difference is statistically significant (Z = 3.32, Z critical = 1.96, P = 0.00090). This indicates that the application of the herbicides affects the bacterial population.

Effects of Chronic Use of Herbicides on Soil Physicochemical and Microbiological Characteristics

Introduction: Herbicide application is a vital strategy of weed control. The effects of these chemicals on the non-target soil microorganisms are very intense; have adverse impact on physicochemical parameters of the soil, which in turn affect soil fertility and plant growth.
 Research Gap: There are insufficient literatures on extensive monitoring of the effects of prolonged herbicides use. Existing literatures concerning analysis of effect of prolonged herbicides application on soil are not comprehensive with respect to number of soil characteristics analyzed.
 Aim: This study assessed the effects of Atrazine and Glyphosate on physicochemical properties and microbial population of carrot and maize farm soils, exposed to prolonged use at Songhai Delta.
 Place and Duration of Study: The study was conducted in Songhai Delta farms and the Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, Effurun, from April to July, 2019.
 Methodology: These pesticides were applied according to the manufacturers’ instructions at sublethal concentrations. Their effects on soil pH, cation exchange capacity, total organic carbon, nitrates, phosphates, sulphates and microbial populations at two depths (0-15 and 15-30 cm) were assessed using standard methods. Microbial counts were carried out for total heterotrophic bacteria and fungi using the pour plate method.
 Results: There were variations in the different properties of the carrot and maize farm soils. Soil pH was higher in maize farm (5.91±0.10) than in carrot farm (5.88±0.06) at the depth of 15-30 cm. The pH, total organic carbon, nitrate content had no significant difference while phosphate and microbial counts were significantly different at P=.05.
 Conclusion: This assessment has shown that the herbicides had no influence on pH, total organic carbon, nitrate but a negative one on bacterial and fungal populations with prolonged use. A modification in physicochemical and microbiological characteristics of soil could be used to predict the fertility and health status of soils.

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities

The use of synthetic pesticides in agriculture is increasingly debated. However, few studies have compared the impact of synthetic pesticides and alternative biopesticides on non-target soil microorganisms playing a central role in soil functioning.We conducted a mesocosm experiment and used high-throughput amplicon sequencing to test the impact of a fungal biopesticide and a synthetic fungicide on the diversity, the taxonomic and functional compositions, and co-occurrence patterns of soil bacterial, fungal and protist communities.Neither the synthetic pesticide nor the biopesticide had a significant effect on microbial α-diversity. However, both types of pesticides decreased the complexity of the soil microbial network. The two pesticides had contrasting impacts on the composition of microbial communities and the identity of key taxa as revealed by microbial network analyses. The biopesticide impacted keystone taxa that structured the soil microbial network. The synthetic pesticide modified biotic interactions favouring taxa that are less efficient at degrading organic compounds. This suggests that the biopesticides and the synthetic pesticide have different impact on soil functioning.Altogether, our study shows that pest management products may have functionally significant impacts on the soil microbiome even if microbial α-diversity is unaffected. It also illustrates the potential of high-throughput sequencing analyses to improve the ecotoxicological risk assessment of pesticides on non-target soil microorganisms.

Respiration induced by substrate and bacteria diversity after application of diuron, hexazinone, and sulfometuron-methyl alone and in mixture

After application, herbicides often reach the soil and affect non-target soil microorganisms, decreasing their population, diversity or affecting metabolic activity. Therefore, laboratory studies were performed to evaluate the effects of diuron, hexazinone and sulfometuron-methyl alone and mixed upon carbon transformation by soil microorganisms in clayey and sandy soils and the effect on bacterial diversity and structure. Control treatment without herbicide application was also performed. Sub-samples from the control and herbicide treatments (10 g – in triplicate) were collected before herbicide application and 7, 14, 28 and 42 days after treatment (DAT), then 1 mL of 14C-glucose solution was applied. The released 14CO2 was trapped in 2 M NaOH solution and the radioactivity was analyzed by liquid scintillation counting (LSC), 12 h after glucose application. The effect of herbicides on bacterial diversity was evaluated by T-RFLP. The experiment was conducted in a complete randomized design. Hexazinone did not affect 14CO2 evolution. Diuron showed a greater 14CO2 evolution in sandy and clayey soil, while sulfometuron-methyl led to an increase in sandy soil, at 42 DAT. A greater evolution of carbon was observed in the treatment with herbicide mixture in sandy soil, compared with the same treatment in clayey soil or control. However, the herbicide mixture application did not affect the soil biological activity measured by the respiration rate induced by substrate. On the other hand, the herbicide mixtures affected the bacterial diversity in both soils, being the strongest effect to diuron and sulfometuron-methyl in clayey soil and hexazinone in sandy soil.

The overexpression of antifungal genes enhances resistance to rhizoctonia solani in transgenic potato plants without affecting arbuscular mycorrhizal symbiosis

The biological control of fungal diseases through the use of genetically modified (GM) plants could decrease the input of chemical pesticides. To overcome possible losses in potato (Solanum tuberosum) yield because of susceptibility to soil fungal pathogens, researchers have developed potato transgenic lines expressing antifungal proteins. However, all GM crops must be monitored in their potentially detrimental effects on non-target soil microorganisms. Arbuscular mycorrhizal (AM) fungi are good candidates for this type of analysis, as good indicators of a normal rhizosphere structure and functionality. In this work, we have monitored potato lines with over-expression of genes encoding peptides with antifungal properties on their effects on the soil-borne fungal pathogen Rhizoctonia solani and AM fungi.The six GM potato lines (AG-1, AG-3, RC-1, RC-5, AGRC-8 and AGRC-12) evaluated showed higher reduction in infection indexes in comparison to untransformed plants when challenged with a highly virulent strain of R. solani. The growth of RC-1, RC-5 and AGRC-12 lines remained almost unaltered by the pathogen; which evidenced the maximum inhibition of R. solani infection. The level of root colonization by the AM fungus Rizophagus intraradices (pure in vitro isolated) did not significantly differ between transgenic and wild potato lines under in vitro and microcosm conditions. An increase in mycorrhization was evident with the addition of potato biomass residues of these GM lines in comparison to the addition of residues of the wild type potato line.In addition to the R. intraradices assays, we performed microcosm assays with soil samples from sites with at least100-year history of potato crop as inoculum source.The roots of AGRC-12 GM line showed significant higher levels of native mycorrhization and arbuscules development. In general, the potato lines apparently were less receptive to R. intraradices pure inoculum than to AM species from the natural inoculum. In this work, the selected GM potato lines did not have evident adverse effects on AM fungal colonization.

Assessment of the ecotoxicological impact of natural and synthetic β-triketone herbicides on the diversity and activity of the soil bacterial community using omic approaches

The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these two herbicides (i.e. dissipation and formation of transformation products) was monitored to assess the scenario of exposure of soil microorganisms to natural and synthetic herbicides. Ecotoxicological impact of both herbicides was explored by monitoring soil bacterial diversity and activity using next-generation sequencing of 16S rRNA gene amplicons and soil metabolomics. Both leptospermone and sulcotrione fully dissipated over the incubation period. During their dissipation, transformation products of natural and synthetic β-triketone were detected. Hydroxy-leptospermone was almost completely dissipated by the end of the experiment, while CMBA, the major metabolite of sulcotrione, remained in soil microcosms. After 8 days of exposure, the diversity and structure of the soil bacterial community treated with leptospermone was significantly modified, while less significant changes were observed for sulcotrione. For both herbicides, the diversity of the soil bacterial community was still not completely recovered by the end of the experiment (45 days). The combined use of next-generation sequencing and metabolomic approaches allowed us to assess the ecotoxicological impact of natural and synthetic pesticides on non-target soil microorganisms and to detect potential biomarkers of soil exposure to β-triketones.

Toxicity of biocides to native cyanobacteria at different rice crop stages in wetland paddy field

Biocides (herbicides and insecticides) are intensively being used in rice cultivation, despite several adverse non-target effects on native cyanobacteria. Comparative effects of three herbicides (benthiocarb, butachlor, and 2,4-D) and four insecticides (furadon, phorate, methyl parathion, and ekalux) were studied at field-recommended doses. Field experiments of rice were carried out for three consecutive seasons in completely randomized block designs in both rainy and winter croppings at the Central Rice Research Institute, Cuttack, India. Toxicities of seven biocides individually to native cyanobacteria growing with rice crops in wetland fields were assessed for growth and acetylene reduction activity (ARA); several crop parameters of paddy were estimated concomitantly. It was observed that applications of butachlor and benthiocarb individually significantly decreased growth (15.86 and 17.50%), ARA (0.16 and 0.68%), and N-yield (0.26 and 0.85%) of the native cyanobacteria, whereas these parameters increased (24.04% in growth, 0.25% in ARA, and 0.40% in N-yield) due to the application of 2,4-D. Of the tested insecticides, furadon, phorate, and methyl parathion enhanced the growth (17.8, 10.7, and 11.7%), N2-fixation (0.10, 0.097, and 0.074%), and N-yield (0.16, 0.18, and 0.20%) of cyanobacteria, whereas ekalux had no significant effect on cyanobacteria. On the basis of cyanobacterial parameters, biocides could be recommended for rice crops in the order furadon < phorate < methyl parathion < ekalux. Applications of 2,4-D and furadon individually in comparison to the rest other biocides enhanced rice yield. These finding could help to revise integrated strategies of weed and pest management in wetland rice agriculture to save non-target soil microorganisms, particularly cyanobacteria.

3,4-Dimethylpyrazole phosphate (DMPP) reduces activity of ammonia oxidizers without adverse effects on non-target soil microorganisms and functions

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is widely used within agriculture to reduce nitrate leaching and improve nitrogen use efficiency of fertilizers, but few studies examined effects on non-target soil functions and microorganisms, i.e. other than the intended delay of ammonia oxidation. We investigated effects of DMPP amendment equivalent to 0 (Control), 1 (regular dose, RD) or 10 (high dose, HD) kgha−1 in a sandy loam grassland soil at 50% water-filled pore space. Following incubation for 1, 7 or 14 d, soil was analyzed for fluorescein diacetate hydrolysis, dehydrogenase activity, phospholipid fatty acid composition and potential ammonia oxidation. DMPP showed no significant non-target effects (p>0.05), but a possible stress response in HD was indicated by a factor analysis of phospholipid fatty acid composition. There was a strong DMPP inhibition on potential ammonia oxidation which was still significant (p<0.05) in HD after 14 d. In separate treatments receiving 50mg NH4+-Nkg−1 dry soil in addition to DMPP, the inhibition of nitrate accumulation was similar in RD and HD at around 75%. Abundances of the gene amoA from ammonia oxidizing bacteria (AOB) and archaea (AOA) were quantified, and cell-specific nitrification rates were estimated. There was a general trend of increasing AOA and AOB abundance towards the end of incubation irrespective of DMPP treatment, whereas cell-specific activity of AOA and/or AOB was reduced in the presence of DMPP. Overall, this study indicated that DMPP effectively inhibited nitrification activity without effects on ammonia oxidizer populations, as well as non-target soil microorganisms or functions.

Resilience of soil microbial and nematode communities after biofumigant treatment with defatted seed meals

The use of alternative biocidal compounds to replace chemical pesticides after the Directive 2009/128/EC has raised renewed interest in the biofumigation technique. In particular, the defatted seed meals (DSM) derived from Brassicaceae plant tissues with high glucosinolate content represent an efficient practice to control soil-born plant pathogens and pests that can be applied in synergy to catch crop green manures. For a wider and safer application of this technique, the impacts on non-target soil microorganisms and free-living nematodes have to be investigated in more depth. In this pot-scale experiment a naturally nematode-infected soil was amended with a glucosinolate-containing DSM from Brassica carinata, a non-glucosinolate-containing DSM from sunflower and the metam-sodium fumigant. Tomato plants were transplanted and checked for the presence of pests and/or pathogens and plant vigour. The response of soil microbial communities was assessed by PCR-DGGE analysis of bacterial 16S rRNA and fungal 18S rRNA genes, whereas nematode indices were applied to assess their community structure 0, 10, 32 and 62 days after the treatments. Significant shifts were observed among both bacterial and fungal communities, whereas various changes of nematode communities occurred depending on the nematode family. Similar changes initially occurred in both bacterial and fungal community structure in response to DSM and VAP amendments, but after 62 days fungal communities were more strongly shaped by VAP fumigation than bacteria. The non-biofumigant SUN treatment added organic matter into the soil inducing significant changes in microbial communities, but it was not effective against Meloidogyne incognita root infestation. Although the free-living nematode structure was negatively influenced by all treatments, B. carinata DMS proved the best compromise between efficiency to control M. incognita and environmental impact. These results confirmed the interesting potential of biofumigant DSM amendments as alternatives to chemical fumigants for a more environment-friendly control of some soil-borne diseases.

Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments

Producers of several high-value crops in California rely heavily on soil fumigants to control key diseases, nematodes, and weeds. Fumigants with broad biocidal activity can affect both target and nontarget soil microorganisms. The ability of nontarget soil microorganisms to recover after fumigation treatment is critical because they play an important role in sustaining the health of agricultural and natural soil systems. Fumigation trial was conducted in Parlier, CA, and the study focuses on the effects of different rates of Telone C35 and also methyl bromide fumigation with polyethylene (PE) and totally impermeable film (TIF) tarps on target and nontarget soil microorganisms using field samples. Results indicated that the populations of target organisms, such asFusarium oxysporumandPythiumspp., were reduced at all rates of fumigants. Phospholipid fatty acid (PLFA) analysis indicated that all major nontarget soil microbial groups such as Gram positive bacteria, Gram negative bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) were affected by methyl bromide (MeBr) fumigation treatment. In general, the effects of Telone C35 (299 L/ha) under PE tarp had the least impact on microbial community structure and better effect on controlling target microorganisms and, therefore, indicated the better option among fumigation treatments.

Effect of tetraconazole application on the soil microbial community

Tetraconazole is one of the most commonly used triazole fungicides in agricultural practice, and its continuous application poses a potential risk for non-target soil microorganisms. Therefore, the objective of this study was to evaluate the effect of tetraconazole at the field rate (T1, 0.33 mgkg(-1) of soil), three times the field rate (T3, 1.00 mgkg(-1) of soil) and 10 times the field rate (T10, 3.33 mgkg(-1) of soil) on the soil microorganisms. To ascertain this effect, the tetraconazole concentration and the microbial properties with potential as bioindicators of soil health (i.e. microbial biomass C, basal respiration, substrate-induced respiration, structure diversity and functional community profiling) were determined. The results showed that the degradation half-lives of tetraconazole varied from 69 to 87 days, depending on the three application concentrations. The microbial biomass C, basal respiration and substrate-induced respiration were inhibited, but they tended to recover at the end of the incubation when tetraconazole was applied at the recommended field rate. The ratios of the gram-negative to gram-positive (GN to GP) bacteria decreased, and the fungi to bacteria ratio increased after a temporal decrease on the seventh day. A principal component analysis of the PLFAs showed that tetraconazole application significantly shifted the microbial community structure on day 7. Different functional community profiles were observed, depending on the tetraconazole application rates. It was concluded that tetraconazole application decreases the soil microbial biomass and activity and changes the structures of the soil microbial community.

Short-term effects of the herbicide napropamide on the activity and structure of the soil microbial community assessed by the multi-approach analysis

Napropamide is one of the most commonly used herbicide in agricultural practice and its continuously application poses a potential risk for non-target soil microorganisms. Therefore, the objective of this study was to assess the impact of napropamide, applied at the field rate (FR, 2.25mgkg−1 of soil) and 10 times the FR (10*FR, 22.5mgkg−1 of soil) on soil microorganisms. To ascertain this impact, substrate-induced respiration (SIR), dehydrogenase (DHA), acid and alkaline phosphatases (PHOS-H and PHOS-OH), urease (URE) activities and changes in concentrations of NO3− and NH4+ ions were determined. In addition, numbers of total bacteria and bacteria involved in soil nitrogen transformation were enumerated. A phospholipid fatty acid (PLFA) method was used to assess changes in the structure of soil microbial communities. Results showed negative effect of napropamide applied at the FR for SIR, the number of total bacteria, DHA, both PHOS, and URE at the beginning of the experiment. In 10*FR treated soil, a decreased activity of SIR, DHA, PHOS-OH and PHOS-H was observed over the experimental period. Nitrifying and N2-fixing bacteria appeared to be the most sensitive to napropamide. The concentration of NO3− decreased in both napropamide-treated soils, whereas the concentration of NH4+ on day 28 in soil with 10*FR was 5 times higher than in the control. Analysis of the PLFA profiles showed that napropamide decreased the biomass of total, bacterial and fungal PLFAs on day 1, while at the end of the experiment in the soil treated with FR dosage of napropamide biomass of total, Gram-negative bacteria and fungi was significantly higher than those observed in the control. A principal component analysis of the PLFAs showed that napropamide application significantly shifted the microbial community structure on days 1 and 14. The degradation kinetics data showed that napropamide degradation by soil autochthonous microorganisms was relatively slow. The results indicated that a broad spectrum of analyze gives a better insight into the true effects of napropamide on soil microorganisms than the single assays.

Successive soil treatment with captan or oxytetracycline affects non-target microorganisms

Changes in microbial biomass and activity were determined in a sandy-loam soil treated with successive dosages of oxytetracycline (a bactericide) or captan (a fungicide) throughout 98 days of incubation under laboratory conditions. The numbers of culturable bacteria and fungi, total bacterial and fungal biomass (as amounts of phospholipid fatty acids, PLFA), the fungal/bacterial ratio, activities of acid and alkaline phosphatases and urease as well as concentrations of N-NH4+ and N-NO3− were assessed. Both oxytetracycline and captan significantly decreased numbers of culturable bacteria whereas total bacterial biomass (bactPLFA) was not affected. Oxytetracycline did not effect on the fungal biomass, however their numbers were reduced after the first and second time of soil amendment with the bactericide. Conversely, fungal numbers and biomass (PLFA 18:2ω6,9) significantly decreased in response to soil treatment with the fungicide. Compared to oxytetracycline, captan significantly decreased activities of acid and alkaline phosphatases. For urease activity, the decreased activity was only observed in the soil after the third dosage of captan. Both biocides significantly increased concentrations of N-NH4+ and decreased concentrations of N-NO3− after the soil treatments. The results of this study indicate that successive soil treatment with oxytetracycline or captan dosages may negatively affect non-target soil microorganisms and their activities.