Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard

Soil management affects carbon and nitrogen concentrations and stable isotope ratios in vine products

Weeds reduce vineyard productivity and affect grape quality by competing with grapevines (Vitis vinifera L.) for water and nutrients. The increased banning of herbicides has prompted the evaluation of alternative soil management strategies. Cover cropping seems to be the best alternative for weed management. However, it may impact vine growth, grape yield, and quality. Quantitative studies on these changes are scarce. Our study aimed to investigate the combined effect of grass cover and water availability on vines of three cultivars, the white Chasselas and Petite Arvine and the red Pinot noir field-grown under identical climatic and pedological conditions and grafted onto the same rootstock. Soil management and irrigation experiments were performed during the 2020-2021 seasons. Two extreme soil management practices were established in the vineyard, based on 100 % bare soil (BS) by the application of herbicides with glufosinate or glyphosate as active ingredients and 100 % grass-covered soil (GS) by cover cropping with a mixture of plant species. Two water statuses were imposed by drip irrigation (DI) and no irrigation (NI). The level of vine-weed competition for water and nitrogen (N) was assessed in the vine, must, and wine solid residues (WSRs) by comparing measurements, i.e., the yeast assimilable N content, C/N_WSR, carbon and N isotope ratios (δ¹³C_grape-sugars, δ¹³C_WSR, and δ¹⁵N_WSR) among the different treatments (BS-DI, BS-NI, GS-DI, GS-NI). The increase in the δ¹³C_grape-sugars and δ¹³C_WSR values with increasing plant water deficit mimicked the observations in irrigation experiments on BS. The N_WSR content and δ¹⁵N_WSR values decreased with water stress and much more strongly in vines on GS. The dramatic N deficit in rainfed vines on GS could be alleviated with irrigation. The present study provides insights from chemical and stable isotope analyses into the potential impact of cover cropping in vineyards in the context of the banning of herbicides in a time of global water scarcity due to climate change.

Impact of pyroxasulfone on sugarcane rhizosphere microbiome and functioning during field degradation

Pyroxasulfone (PYR) is a widely used herbicide, but its effects on non-target organisms, particularly microorganisms, are largely unknown. Herein, we investigated the effects of various doses of PYR on the sugarcane rhizosphere microbiome by using amplicon sequencing of rRNA genes and quantitative PCR techniques. Correlation analyses indicated that several bacterial phyla (Verrucomicrobia and Rhodothermaeota) and genera (Streptomyces and Ignavibacteria) strongly responded to PYR application. Additionally, we found that both bacterial diversity and composition were significantly altered after 30 days, indicating a prolonged effect of the herbicide. Moreover, co-occurrence analyses of the bacterial community showed that the network complexity was significantly decreased by PYR at day 45. Furthermore, FAPROTAX analysis suggested that some functions with implications for carbon cycling groups were significantly altered after 30 days. Overall, we provide the first indications that PYR may not pose a significant risk for altering microbial communities in the short term (less than 30 days). However, its potential negative effects on bacterial communities in the middle and late stages of degradation deserve further attention. To our knowledge, this is the first study to provide insight into the effects of PYR on the rhizosphere microbiome, providing an extended basis for future risk assessments.

Overhauling the ecotoxicological impact of synthetic pesticides using plants' natural products: a focus on Zanthoxylum metabolites

The reduction in agricultural production due to the negative impact of insects and weeds, as well as the health and economic burden associated with vector-borne diseases, has promoted the wide use of chemicals that control these "enemies." However, the use of these synthetic chemicals has been recognized to elicit negative impacts on the environment as well as the health and wellbeing of man. In this study, we presented an overview of recent updates on the environmental and health impacts of synthetic pesticides against agro-pest and disease vectors while exhaustive reviewing the potentials of natural plant products from Zanthoxylum species (Rutaceae) as sustainable alternatives. This study is expected to spur further research on exploiting these plants and their chemicals as safe and effective pesticide entities to minimize the impact of their chemical and synthetic counterparts on health and the environment.

Ecotoxicological relevance of glyphosate and flazasulfuron to soil habitat and retention functions - Single vs combined exposures

Glyphosate (GLY) and flazasulfuron (FLA) are two non-selective herbicides commonly applied together. However, research focused on their single and combined ecotoxicological impacts towards non-target organisms is still inconclusive. Therefore, this study aimed to test their single effects on soil's habitat and retention functions, and to unravel their combined impacts to earthworms and terrestrial plants. For this, ecotoxicological assays were performed with plants (Medicago sativa), oligochaetes (Eisenia fetida) and collembola (Folsomia candida). Soil elutriates were also prepared and tested in macrophytes (Lemna minor) and microalgae (Raphidocelis subcapitata). FLA (82-413 µg kg^-1) reduced earthworms' and collembola's reproduction and severely impaired M. sativa growth, being much more toxic than GLY (up to 30 mg kg^-1). In fact, the latter only affected plant growth (≥ 9 mg kg^-1) and earthworms (≥ 13 mg kg^-1), especially at high concentrations, with no effects on collembola. Moreover, only elutriates from FLA-contaminated soils significantly impacted L. minor and R. sucapitata. The experiments revealed that the co-exposure to GLY and FLA enhanced the toxic effects of contaminated soils not only on plants but also on earthworms'. However, such increase in toxicity was dependent on GLY residual concentrations in soils. Overall, this work underpins that herbicides risk assessment should consider herbicides co-exposures, since the evaluation of single exposures is not representative of current phytosanitary practices and of the potential effects under field conditions, where residues of different compounds may persist in soils.

Effervescent powder-assisted floating organic solvent-based dispersive liquid-liquid microextraction for determination of organochlorine pesticides in water by GC-MS

An effervescent powder-assisted floating organic solvent-based dispersive liquid-liquid microextraction was introduced for determination of 13 organochlorine pesticides in water samples. In this method, a less toxic low-density organic solvent was used as extraction solvent. The extraction solvent was dispersed in to the aqueous sample via CO₂ bubbles, in-situ generated up on addition of water to a falcon tube containing the mixture of effervescent powder precursors as well as the extraction solvent. Various experimental parameters such as effervescent and its weight fractions, extraction solvent type and its volume, the total mass of effervescent precursors, and the effect of salt were investigated and the optimal conditions were established. Under the optimum conditions, the proposed method exhibited good linearity for all target pesticides with the coefficient of determinations varying from 0.9981 to 0.9997. The limits of detection and quantification were within the range of 0.03-0.24 and 0.26-0.75 μg/L, respectively. The intra- and inter-day precisions which were expressed in terms of the relative standard deviation ranged from 0.33 to 4.47 and 0.51-5.52%, respectively. The enrichment factors and recoveries ranged from 24 to 293 and 76-116%, respectively. The proposed method could be used simple, cheap, fast, and environmentally friendly alternative for analysis of organochlorine pesticides from environmental water and other similar matrices.

Vineyard Management and Its Impacts on Soil Biodiversity, Functions, and Ecosystem Services

Healthy soils form the basis of sustainable viticulture, where soil characteristics have a direct impact on wine quantity and quality. Soil not only provides water and nutrients to vines, but is also a living medium containing micro- and macroorganisms that perform many ecological functions and provide ecosystem services. These organisms are involved in many processes, from decomposing organic matter to providing minerals to vine roots. They also control diseases, pests, and weeds, in addition to improving the soil structure in terms of its capacity to retain water and nutrients. Related to decomposition processes, the carbon content of vineyard soils influences fertility, erosion and biogeochemical cycles, with significant implications for the global climate. However, common agricultural practices represent strong threats to biodiversity and associated ecosystem services provided by vineyard soils. As consumers increasingly consider environmental aspects in their purchase decisions, winegrowers have to adapt their vineyard management strategies, raising the demand for sustainable pest- and weed-control methods. This article presents a comprehensive review of the impacts of vineyard practices on the soil ecosystem, biodiversity, and biodiversity-based ecosystem services, and provides future prospects for sustainable viticulture.

Microbiomes and glyphosate biodegradation in edaphic and aquatic environments: recent issues and trends

Glyphosate (N-(phosphonomethyl)glycine) has emerged as the top-selling herbicide worldwide because of its versatility in controlling annual and perennial weeds and the extensive use of glyphosate-resistant crops. Concerns related to the widespread use of glyphosate and its ubiquitous presence in the environment has led to a large number of studies and reviews, which examined the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA) in the environment. Because the biological breakdown of glyphosate is most likely the main elimination process, the biodegradation of glyphosate has also been the object of abundant experimental work. Importantly, glyphosate biodegradation in aquatic and soil ecosystems is affected not only by the composition and the activity of microbial communities, but also by the physical environment. However, the interplay between microbiomes and glyphosate biodegradation in edaphic and aquatic environments has rarely been considered before. The proposed minireview aims at filling this gap. We summarize the most recent work exploring glyphosate biodegradation in natural aquatic biofilms, the biological, chemical and physical factors and processes playing on the adsorption, transport and biodegradation of glyphosate at different levels of soil organization and under different agricultural managements, and its impact on soil microbial communities.

Ecotoxicity of herbicide carfentrazone-ethyl towards earthworm Eisenia fetida in soil

Herbicides pose a potential threat to the soil biodiversity and health. Carfentrazone-ethyl (CE), a triazolinones herbicide, is increasingly used in agricultural production. Its non-target toxic effects on soil microorganisms and soil enzymes are reported recently. However, the sublethal toxicity of CE on soil invertebrates like earthworms is not yet known. Therefore, in this work, the sublethal toxic effects of CE (0.05, 0.5, and 5.0 μg/g in soil) on the soil earthworm (Eisenia fetida) were evaluated using a battery of biomarkers including reactive oxygen species (ROS), enzyme (superoxide dismutase-SOD, catalase-CAT, peroxidase-POD, and glutathione S-transferase-GST) activities, malondialdehyde (MDA) contents, histopathological and DNA damage. Results indicated that CE increased ROS contents, enzyme activities, and MDA contents in the short-time (14 d), thus, causing a slight oxidative stress to E. fetida. However, the toxic effects of CE on earthworms gradually disappeared after 14 days. The CE did not cause histopathological and DNA damage in earthworms. Integrated Biological Response index (IBR) indicated that both concentration and exposure time of CE regulated its sublethal toxicity on earthworms. In conclusion, herbicide CE is safe to soil invertebrate earthworms when applied at the recommended doses. Our results contribute to the current understanding of CE effects on soil earthworms, and can be useful in developing soil health strategies under agrochemical use.

Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.

Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes

With the recent advancement of next-generation sequencing methods, there has been an increase in studies on identification of vineyard microbiota, winery-associated microbiota, and microbiota in wine fermentation. However, there have been few studies investigating the fungal microbiota of table grapes which present distinct spoilage and food safety challenges. The aims of this study were to identify and compare the impact of year, variety, and vineyard location on grape, leaf, and soil fungal communities of two varieties of table grapes, Faith and Gratitude, grown in two open-air vineyards and one high tunnel vineyard. The grape, leaf, and soil mycobiota were analyzed using high throughput amplicon sequencing of the ITS region. The sampling year and location of table grapes had an impact on grape, leaf, and soil mycobiota. Fungal diversity of grape, leaf, and soil was greater in 2017 than in 2016. Grape and leaf samples presented strong similarities in fungal communities with abundance of Sporidiobolaceae and Filobasidium in two vineyards and Cladosporium in another one. The high tunnel structure had distinct grape and leaf fungal communities compared to the two other vineyard locations. Mortierella was the predominant genus (27%) in soil samples for the three locations; however, genera of lower abundance varied between locations. These results provide extensive description of fungal communities in less-studied table grape vineyards and high tunnels, providing useful insight of potential threats and preventive strategies to help improve the production and marketability of table grapes.

Mucoromycotina Fungi Possess the Ability to Utilize Plant Sucrose as a Carbon Source: Evidence From Gongronella sp. w5

Mucoromycotina is one of the earliest fungi to establish a mutualistic relationship with plants in the ancient land. However, the detailed information on their carbon supply from the host plants is largely unknown. In this research, a free-living Mucoromycotina called Gongronella sp. w5 (w5) was employed to explore its effect on Medicago truncatula growth and carbon source utilization from its host plant during the interaction process. W5 promoted M. truncatula growth and caused the sucrose accumulation in M. truncatula root tissue at 16 days post-inoculation (dpi). The transportation of photosynthetic product sucrose to the rhizosphere by M. truncatula root cells seemed accelerated by upregulating the SWEET gene. A predicted cytoplasmic invertase (GspInv) gene and a sucrose transporter (GspSUT1) homology gene in the w5 genome upregulated significantly at the transcriptional level during w5–M. truncatula interaction at 16 dpi, indicating the possibility of utilizing plant sucrose directly by w5 as the carbon source. Further investigation showed that the purified GspInv displayed an optimal pH of 5.0 and a specific activity of 3380 ± 26 U/mg toward sucrose. The heterologous expression of GspInv and GspSUT1 in Saccharomyces cerevisiae confirmed the function of GspInv as invertase and GspSUT1 as sugar transporter with high affinity to sucrose in vivo. Phylogenetic tree analysis showed that the ability of Mucoromycotina to utilize sucrose from its host plant underwent a process of “loss and gain.” These results demonstrated the capacity of Mucoromycotina to interact with extant land higher plants and may employ a novel strategy of directly up-taking and assimilating sucrose from the host plant during the interaction.

Sustainable Viticulture: Effects of Soil Management in Vitis vinifera

Soil management in vineyards is of fundamental importance not only for the productivity and quality of grapes, both in biological and conventional management, but also for greater sustainability of the production. Conservative soil management techniques play an important role, compared to conventional tillage, in order to preserve biodiversity, to save soil fertility, and to keep vegetative-productive balance. Thus, it is necessary to evaluate long-term adaptation strategies to create a balance between the vine and the surrounding environment. This work sought to assess the effects of following different management practices on Vitis vinifera L. cv. Cabernet Sauvignon during 2017 and 2018 seasons: soil tillage (T), temporary cover cropping over all inter-rows (C), and mulching with plant residues every other row (M). The main physiological parameters of vines (leaf gas exchange, stem water potential, chlorophyll fluorescence, and indirect chlorophyll content) as well as qualitative and quantitative grape parameters (technological and phenolic analyses) were measured. Significant differences in gas exchanges related to the different season and inter-row management were observed. C showed more negative values of water potential, due to the grass–vine competition, especially when water availability was lower. The competition exerted by C led to differences in fruit setting with impact on yield; therefrom, significant differences also in sugar and anthocyanic content were observed.

Isolation of culturable mycota from Argentinean soils exposed or not-exposed to pesticides and determination of glyphosate tolerance of fungal species in media supplied with the herbicide

The current agricultural system has led to the development of glyphosate (GP)-resistant weeds, causing an increase in GP doses and applications. Native mycota of pesticide-contaminated sites are the major source of pesticide-degrading microorganisms. The aims of the present study were to isolate the GP-tolerant culturable mycota in two soils with different pesticide exposure from Córdoba, Argentina, and to evaluate the growth parameters in native fungal isolates in the presence of GP and the effective dose that caused 50% growth reduction. The results showed that the genera Fusarium, Aspergillus, Mucor, Penicillium and Sterilia were the prevalent fungi isolated from soils both exposed and not-exposed to pesticides. The highest value (>100mM) of effective concentration of herbicide that caused 50% growth inhibition (EC50), was found for Trichoderma isolates. Sterilia spp. had EC50 values of 100mM, while Aspergillus spp. and Mucor had EC50 values between 50 and 100mM. The growth rate evaluation varied according to the isolates and GP concentrations. The data showed that all Aspergillus spp., Trichoderma spp., Mucor and three Sterilia spp. had the best growth performance in media supplied with GP after a variable acclimation period. This study provides valuable data for further studies that would allow to know the metabolic capacity of these fungal species that can be potential candidates for GP removal from contaminated environments.

Commercial glyphosate-based herbicides effects on springtails (Collembola) differ from those of their respective active ingredients and vary with soil organic matter content

Glyphosate-based herbicides (GBH) are currently the most widely used agrochemicals for weed control. Environmental risk assessments (ERA) on nontarget organisms mostly consider the active ingredients (AIs) of these herbicides, while much less is known on effects of commercial GBH formulations that are actually applied in the field. Moreover, it is largely unknown to what extent different soil characteristics alter potential side effects of herbicides. We conducted a greenhouse experiment growing a model weed population of Amaranthus retroflexus in arable field soil with either 3.0 or 4.1% soil organic matter (SOM) content and treated these weeds either with GBHs (Roundup LB Plus, Touchdown Quattro, Roundup PowerFlex) or their respective AIs (isopropylammonium, diammonium or potassium salts of glyphosate) at recommended dosages. Control pots were mechanically weeded. Nontarget effects were assessed on the surface activity of the springtail species Sminthurinus niger (pitfall trapping) and litter decomposition in the soil (teabag approach). Both GBHs and AIs increased the surface activity of springtails compared to control pots; springtail activity was higher under GBHs than under corresponding AIs. Stimulation of springtail activity was much higher in soil with higher SOM content than with low SOM content (significant treatment x SOM interaction). Litter decomposition was unaffected by GBHs, AIs or SOM levels. We suggest that ERAs for pesticides should be performed with actually applied herbicides rather than only on AIs and should also consider influences of different soil properties.

Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance

Glyphosate-based herbicides, such as Roundup®, are the most widely used non-selective, broad-spectrum herbicides. The release of these compounds in large amounts into the environment is susceptible to affect soil quality and health, especially because of the non-target effects on a large range of organisms including soil microorganisms. The soil filamentous fungus Aspergillus nidulans, a well-characterized experimental model organism that can be used as a bio-indicator for agricultural soil health, has been previously shown to be highly affected by Roundup GT Plus (R450: 450 g/L of glyphosate) at concentrations far below recommended agricultural application rate, including at a dose that does not cause any macroscopic effect. In this study, we determined alterations in the transcriptome of A. nidulans when exposed to R450 at a dose corresponding to the no-observed-adverse-effect level (NOAEL) for macroscopic parameters. A total of 1816 distinct genes had their expression altered. The most affected biological functions were protein synthesis, amino acids and secondary metabolisms, stress response, as well as detoxification pathways through cytochromes P450, glutathione-S-transferases, and ABC transporters. These results partly explain the molecular mechanisms underlying alterations in growth parameters detected at higher concentrations for this ascomycete fungus. In conclusion, our results highlight molecular disturbances in a soil fungus under conditions of apparent tolerance to the herbicide, and thus confirm the need to question the principle of "substantial equivalence" when applied to plants made tolerant to herbicides.