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Gram positive bacteria, Gram negative bacteria, fungal, arbuscular mycorrhizal fungi (AMF), and actinomycetes phospholipid fatty acids (PLFAs) for microplot trial. Different letters indicate significant differences (P < 0.05). Error bars indicate standard error. Dimethyl disulfide (DMDS) was applied at 0 (control), 32, 64, 128, or 256 mg a.i. L −1 air space per vine and samples were taken 15, 45, 60, and 90 d after fumigation.
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information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. D imethyl disulfide (DMDS) is a relatively new compound in agriculture that has zero ozone depletion potential (Gillis, 2003) and is a sulfur vola-ti...
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Citations
... No significant differences in CEC, soil pH, P, Ca, Mg, NO 3 − , and NH 4 + were detected between treatments in 2020 (Supplementary Table S1A) and in 2021 (Supplementary Table S1B). Previous studies across different crops and environmental conditions have also reported limited impacts of fumigants on soil properties and when they do occur, they often disappear approximately 30 days after fumigation (Dangi et al., 2014;Fang et al., 2018Fang et al., , 2019Fang et al., , 2020. This could be due to the short halflife of these products in soil (Dungan et al., 2003;Castellano-Hinojosa et al., 2022a). ...
Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.
... S -methyl L -cysteine sulfoxide, a derivative of s-methyl L-cysteine, is an attractant for plant parasitic nematodes [62], which reduce plant growth and productivity. However, s-methyl L-cysteine sulfoxide, a precursor of the soil fumigant dimethyldisulide (DMDS) [63], is produced by plants [64] and bacteria [65]. Although DMDS is a soil fumigant that controls soil-borne pathogens and nematodes, it has been pointed out that it may not function depending on the microbial environment of the soil [63]. ...
... However, s-methyl L-cysteine sulfoxide, a precursor of the soil fumigant dimethyldisulide (DMDS) [63], is produced by plants [64] and bacteria [65]. Although DMDS is a soil fumigant that controls soil-borne pathogens and nematodes, it has been pointed out that it may not function depending on the microbial environment of the soil [63]. Therefore, investigating the significance of these metabolites is an interesting perspective. ...
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
... Previous studies have shown that soil microbial communities recovered relatively rapidly after soil fumigation (Dangi et al. 2014(Dangi et al. , 2015Liu et al. 2015;Rokunuzzaman et al. 2016;Fang et al. 2018;Zhang et al. 2019). Zhang et al. (2017a, b) found that after repeated application of soil fumigants, susceptible soil microbes could disappear while the proportion of those tolerant microbes could increase gradually and even eventually dominate the soil microbiome. ...
Purpose
Although soil fumigation efficiently controls soil-borne diseases, the effects of repeated soil fumigation on soil phosphorus (P) cycling are still largely unknown.
Methods
In this study we conducted a field experiment to explore soil phosphorus availability in ginger fields with 0, 3, and 7 years (F0, F3, and F7) of annual chloropicrin (CP) fumigation history in Shandong Province of China. Soil samples (0–20 cm) were collected at four different times in 2019. Ginger yield, soil phosphatase (acid and alkaline) activities, and soil P fractions were measured.
Results
Results showed that ginger rhizome yield was similar in F0 and F3 (70.0 t ha ⁻¹ ), but significantly lower in F7 (37.5 t ha ⁻¹ ). The acid phosphatase (AiP) activity was significantly higher in F0, while alkaline phosphatase (AlP) activity was the highest in F3. There was no significant difference in the available P (resin-P + NaHCO 3 -P + NaOH-P) between F0 and F7, with 33.6 to 57.5% of total P (TP), while the available P was significantly lower in F3, being less than 30% of TP. Redundancy analysis (RDA) showed that the highest pH values in F3 contributed to the lowest soil P availability there. AiP activities showed highly positive effects on the soil labile P contents.
Conclusion
Results suggested that more P fertilizers are needed after 3 years of CP fumigation to avoid soil P deficiency for ginger growth. The death of ginger became the main limitation for ginger production after 7 years of CP fumigation, at which time, comprehensive agricultural practices should be considered to control ginger soil-borne diseases.
... Microorganisms in the soil contribute significantly to organic matter decomposition, soil structure, soil quality, nutrient cycling, and plant nutrient uptake, and it is very important for them to recover after treatment with biocidal soil fumigants for the development of the long-term health of agricultural soils (Dangi, Tirado-Corbalá, Cabrera, Wang, & Gerik, 2014;Dangi, Tirado-Corbalá, Gerik, & Hanson, 2017). Therefore, it is important to know the impact of fumigants on both the target soil pathogens and beneficial soil microbial communities, and to gain a broad understanding of the biocidal activity of these fumigants. ...
... Previous studies on the effect of fumigation on soil microorganisms have been conducted in annual crop systems such as in strawberries (Fragaria L.). The long-term fumigation response on soil microbial communities in grapevine has not been studied in detail, except for some short-term studies on dimethyl disulfide by Dangi et al. (2014) or studies on specific microorganisms such as AMF by Menge, Stierle, Bagyaraj, Johnson, and Leonard (1978) and Megne et al. (1983). Grapevine 'sroot distribution is deeper and more extensive than that of annual crops, which may support rhizodeposition at depth, and soil microbial community biomass and structure would differ from crops with shallower rooting depths. ...
California is the number one producer of grapes in the United States. Soil fumigation has been used to control soilborne pests and pathogens. However, fumigants can potentially have a negative impact on native soil microbial populations. Given the roles of microorganisms in the soil system, it is important to assess the long‐term impact of fumigation on soil microbial communities, which is currently lacking. The objective of this research was to study the long‐term impact of microbial communities in grapevine (Vitis vinifera L.) replanting situations after fumigation. Soil treatments included methyl bromide (MeBr), Telone C35, InLine, a nonfumigated control, and a mustard (Sinapis alba L.) cover crop in two side‐by‐side field experiments fumigated in 2007 and 2008. Microbial community biomass in 2017 and 2018 did not differ between fumigated and nonfumigated plots at the 0‐ to 30‐cm depth. However, plots with shank‐injected MeBr and Telone C35 applied in 2008 showed significantly reduced microbial biomass in 2018 at deeper depths than subsurface drip‐applied InLine plots. The results show the impact of fumigation on bacterial communities; however, the impact on fungal and arbuscular mycorrhizal fungi (AMF) communities was not evident after 10 years. Furthermore, the effect of depth was apparent on bacterial communities compared with fungal and AMF communities. The data suggest that deep‐rooted grapevines influenced fungal populations, which probably supplied labile C in fumigated and nonfumigated plots. Future research needs to focus collectively on the long‐term effects of fumigation on fruit quality and yield in vineyards, and on soil microbial communities.
... Several short-term studies on the recovery of soil microbial communities in fumigated fields concluded that soil microbial communities make a relatively rapid recovery (less than a year) after the application of fumigants [9][10][11][12]. However, there are limited studies on the effect of long-term, repeated application of fumigants on soil microbial communities. ...
... It is important to study the effect of fumigants on soil microbial communities in regularly-fumigated fields, as soil microorganisms are crucial in sustaining long-term health of agricultural soil [9]. Hence, understanding the impact of fumigants on beneficial soil microbial communities is essential to help further preserve the health and sustainability of these fumigated lands. ...
High value crop producers in California rely heavily on soil fumigation to control a wide array of soil borne pests including nematodes, pathogens and weeds. Fumigants with broad biocidal activity can affect soil microbial communities that contribute to nutrient cycling and plant nutrient uptake which can impact soil health. It is often thought that soil microbial communities make a relatively rapid recovery following fumigation. However, recently it has been found that repeated application of fumigants over time can have greater and longer lasting impacts on soil microorganisms than single fumigation events. Therefore, the main objective of this study was to determine the effect of long-term repeated application of fumigants on soil microbial communities and compare them with non-fumigated and organic sites. Soil samples were collected from fields in Watsonville, CA. Chronosequence sites were defined by number of years of annual fumigation (yaf) with methyl bromide (15, 26, 33, 39 yaf) at the time of sampling, and representative non-fumigated sites were also included for comparison. Phospholipid fatty acid (PLFA) analysis was used to analyze the samples. The canonical variate analysis showed that microbial communities in sites with a longer history of fumigation (33 and 39 yaf) were similar to one another; however, they differed significantly from 15 yaf site and further analysis concluded that non-fumigated sites were significantly different than fumigated sites. This study showed that the proportion of arbuscular mycorrhizal fungi (AMF) was lower in all fumigated (15, 33 and 39 yaf) sites as compared to their non-fumigated counterparts, which could be a threat to sustainability since AMF plays a major role in soil health and quality.
... For example, Chander and Joergensen (2007) reported no negative effects of Se on soil microbial biomass C and adenosine triphosphate (ATP) concentrations, which contradicts research findings by Frankenberger and Karlson (1994) who showed that microbialinduced volatilization of Se was a protection strategy to avoid toxicity in seleniferous environments. If the soil microorganisms play a role in nutrient cycling and organic matter decomposition (Dangi et al., 2014), they may also participate in transforming or incorporating organic forms of Se into plant available Se (Martens and Suarez, 1997). Similarly, Lindblom et al. (2013) reported that Se tolerant rhizosphere bacteria can boost Se accumulating ability in Brassica juncea (L.) Czern, as well as affect localization and speciation of Se in the roots of Se hyperaccumulators. ...
Selenium (Se) biofortification has been practiced in Se-deficient regions throughout the world primarily by adding inorganic sources of Se to the soil. Considering the use of adding organic sources of Se could be useful as an alternative Se amendment for the production of Se-biofortified food crops. In this multi-year micro-plot study, we investigate growing carrots and broccoli in soils that had been previously amended with Se-enriched Stanleya pinnata Pursh (Britton) three and 4 years prior to planting one and two, respectively. Results showed that total and extractable Se concentrations in soils (0–30 cm) were 1.65 mg kg⁻¹ and 88 μg L⁻¹, and 0.92 mg kg⁻¹ and 48.6 μg L⁻¹ at the beginning of the growing season for planting one and two, respectively. After each respective growing season, total Se concentrations in the broccoli florets and carrots ranged from 6.99 to 7.83 mg kg⁻¹ and 3.15 to 6.25 mg kg⁻¹ in planting one and two, respectively. In broccoli and carrot plant tissues, SeMet (selenomethionine) was the predominant selenoamino acid identified in Se aqueous extracts. In postharvest soils from planting one, phospholipid fatty acid (PLFA) analyses showed that amending the soil with S. pinnata exerted no effect on the microbial biomass, AMF (arbuscular mycorrhizal fungi), actinomycetes and Gram-positive and bacterial PLFA at both 0–5 and 0–30 cm, respectively, 3 years later. Successfully producing Se-enriched broccoli and carrots 3 and 4 years later after amending soil with Se-enriched S. pinnata clearly demonstrates its potential source as an organic Se enriched fertilizer for Se-deficient regions.
Background
An insight into the soil microbial functions and spatial distribution of soil resources is an important basis for evaluating and managing plant growth in subtropical forests. Soil samples were collected from five forest stands in Jinyun Mountain Natural Reserve (JMNR) in Chongqing located at the Three Gorges Reservoir area: Gordonia acuminata evergreen broad-leaved forest (GAEBF), Cunninghamia lanceolata forest (CLF), Phyllostachys pubescens forest (PPF), coniferous and broad-leaved mixed forest (CBLMF) dominated by Pinus massoniana and Gordonia acuminata (PM&GA), and the CBLMF dominated by Pinus massoniana and Symplocos setchuensis (PM&SS). Combined with phospholipid fatty acid (PLFA) analysis and Sherlock microbial identification system (MIS), the structure of soil microbial communities in different forest stands was investigated.ResultsThe results showed that the PLFAs of soil microorganisms under the forest in JMNR have a high diversity. The PLFA dominance values of the five stands were 16:0, 19:0 cyclo ω7c, 18:0, 15:0 iso and 16 :0 10-methyl. Furthermore, soil microorganisms are dominated by Gram-negative bacteria, and the PLFAs content of soil bacteria in different forest stands is higher than that of fungi PLFAs. Regarding the phospholipid fatty acid biomarkers, the two CBLMFs are the highest, followed by CLF and GAEBF and PPF is the least. Moreover, the proportion of microorganisms in the soil of different forest stands varies. Among them, MP&SS has the highest gram-negative bacteria, gram-positive bacteria, actinomycetes and fungi.ConclusionsRDA analysis shows that the main influencing factors of PLFAs in the soil of different forest stands are the content of iron oxide, aluminium oxide, organic matter and total nitrogen in the soil, which are considered to be able to reflect the soil nutrient status of JMNR effectively.
Poplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g., selenium (Se) from poor quality soils. Soil microorganisms may play a vital role in sustaining health of soil and/or tolerance of these trees grown in poor quality soils by contributing to nutrient cycling, soil structure, overall soil quality and plant survival. The effect of naturally-occurring salts, boron (B) and Se on soil microbial community composition associated with poplar trees is not known for bioremediation strategies. In this study, three Populus clones: 13-366, 345-1, and 347-14 were grown in spring 2006 under highly saline, B and Se clay-like soils in the west side of the San Joaquin Valley (SJV) of CA, as well as in non-saline sandy loam soils located in the east side of the SJV. After 7 years of growing in the respective soils of different quality, soil samples were collected from poplar clones grown in saline and non-saline soils to examine and compare soil quality effects on soil microbial community biomass and composition. Phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition in soils from trees grown at both locations. This study showed that microbial biomass as well as the amount and proportion of arbuscular mycorrhizal fungal (AMF) community were lower in all three poplar clones grown in saline soil compared to non-saline soil. Amounts of Gram + bacterial and actinomycetes PLFAs were significantly lower in poplar clone 13-366 grown in saline soil compared to non-saline soil; however, they did not differ significantly in poplar clones 347-14 and 345-1. Additionally, amounts of saprophytic fungal, Gram - bacterial and eukaryotic PLFA remained similar at saline and non-saline sites under poplar clones 347-14, 345-1 and 13-366. Therefore, this study suggested that salinity and B do have an impact on microbial biomass and AMF, however, these poplar clones still recycled sufficient amount of nutrients to support and protect saprophytic fungal and bacterial communities from the effects of poor quality soils.
Soil fumigants constitute a major tool for the control of soil borne fungal plant pathogens in protected crops. Dimethyl disulfide (DMDS) is a novel soil fumigant used either alone or in combination with other fumigants for the control of soil borne pests and diseases. In a commercial greenhouse for tomato production, we evaluated the impact of DMDS, comparatively to the alternative fumigant metam sodium, on the population of the dominant fungal plant pathogens in the study soil via q-PCR. Prior to soil fumigation, estimation of the fungal diversity in the studied soil via clone libraries identified Fusarium oxysporum and Rhizoctonia solani as the most abundant soil borne plant pathogens, while Cladosporium spp., known as opportunistic airborne tomato pathogens, were the most dominant fungi and based on this their dynamics upon fumigation was also studied. DMDS, at two dose rates, induced a drastic reduction in the population of F. oxysporum and R. solani, which lasted for the whole cultivation season. On the contrary, metam sodium exhibited an inhibitory effect on F. oxysporum that was alleviated at 120 d post fumigation. Both DMDS and metam sodium induced only a temporal reduction in the soil population of Cladosporium sp. which recovered by 60 days post fumigation. Our data suggest that DMDS even at the low dose rate (56.4 g m−2) could drastically reduce the population of the major soil borne tomato pathogens F. oxysporum and R. solani. Establishment of population thresholds as determined by q-PCR could represent a valuable tool for the estimation of the risk for disease severity and crop yield losses.
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 as Fusarium oxysporum and Pythium spp., 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
