Degradation of the Herbicide Glyphosate by Members of the Family Rhizobiaceae

Effects of herbicides and fertilization on biofilms of Pampean lotic systems: A microcosm study

We experimentally assessed the impact of the application of herbicides and fertilizers derived from agricultural activity through the individual and simultaneous addition of glyphosate, atrazine, and nutrients (nitrogen 'N' and phosphorus 'P') on the biofilm community and their resilience when the experimental factors were removed. We hypothesize that i) the presence of agrochemicals negatively affects the biofilm community leading to the simplification of the community structure; ii) the individual or simultaneous addition of herbicides and nutrients produces differential responses in the biofilm; and iii) the degree of biofilm recovery differs according to the treatment applied. Environmentally relevant concentrations of glyphosate (0.7 mgL-1), atrazine (44 μgL-1), phosphorus (1 mg P L-1 [KH2PO4]), and nitrogen (3 mg N L-1[NaNO3]) were used. Chlorophyll a, ash-free dry weight, abundance of main biofilm groups and nutrient contents in biofilm were analyzed. At initial exposure time, all treatments were dominated by Cyanobacteria; through the exposure period, it was observed a progressive replacement by Bacillariophyceae. This replacement occurred on day 3 for the control and was differentially delayed in all herbicides and/or nutrient treatments in which the abundance of cyanobacteria remains significant yet in T5. A significant correlation was observed between the abundance of cyanobacteria and the concentration of atrazine, suggesting that this group is less sensitive than diatoms. The presence of agrochemicals exerted differential effects on the different algal groups. Herbicides contributed to phosphorus and nitrogen inputs. The most frequently observed interactions between experimental factors (nutrients and herbicides) was additivity excepting for species richness (antagonistic effect). In the final recovery time, no significant differences were found between the treatments and the control in most of the evaluated parameters, evincing the resilience of the community.

Influence of glyphosate and aminomethylphosphonic acid on the mobility of trace elements in uncontaminated and contaminated agricultural soils

Glyphosate is one of the most widely used herbicides in the world. In addition to its herbicidal effect, glyphosate is a chelating agent that can form complexes with trace elements. Yet, agricultural soils can be contaminated with both organic and mineral substances, questioning the possible influence of glyphosate application on the trace element mobility. In this context, we specifically studied the extractability of trace elements in uncontaminated and metal-contaminated agricultural soils by adding glyphosate, formulated glyphosate, and aminomethylphosphonic acid (AMPA, a degradation product of glyphosate) in batch experiments from 0 to 100 mg L-1. Results showed that, on average, glyphosate enhanced the extractability of the elements considered (e.g., As, Cd, Cu, Pb, and Zn) at 20 and 100 mg L-1. Surprisingly, the uncontaminated soil highlighted the highest influence of glyphosate compared to the contaminated ones, likely resulting from a higher natural element extractability in the contaminated soils. Although formulated glyphosate presented an overall higher impact than unformulated glyphosate, it was evidenced that AMPA showed lower influence meaning that glyphosate degradation is beneficial to limit deleterious effects.

Biodegradation characteristics and mechanism of terbuthylazine by the newly isolated Agrobacterium rhizogenes strain AT13

Terbuthylazine (TBA) is an emerging environmental contaminant that poses moderate to high risk to non-target organisms. In this study, a newly TBA-degrading strain, Agrobacterium rhizogenes AT13, was isolated. This bacterium degraded 98.7% of TBA (100 mg/L) within 39 h. Based on the six detected metabolites, three novel pathways of strain AT13, including dealkylation, deamination-hydroxylation, and ring-opening reactions, were proposed. The risk assessment demonstrated that most degradation products might be substantially less harmful than TBA. Whole-genome sequencing and RT-qPCR analysis revealed that ttzA, which encodes S-adenosylhomocysteine deaminase (TtzA), is closely related to TBA degradation in AT13. Recombinant TtzA showed 75.3% degradation of 50 mg/L of TBA within 13 h and presented a K_m value of 0.299 mmol/L and a V_max value of 0.041 mmol/L/min. The molecular docking results indicated that the binding energy of TtzA to TBA was -32.9 kcal/mol and TtzA residue ASP161 formed two hydrogen bonds with TBA at distances of 2.23 and 1.80 Å. Moreover, AT13 efficiently degraded TBA in water and soil. Overall, this study provides a foundation for the characterization and mechanism of TBA biodegradation and may enhance our understanding of the TBA biodegradation by microbes.

Detoxification and metabolism of glyphosate by a Pseudomonas sp. via biogenic manganese oxidation

Biogenic manganese oxides (BMO) are widely distributed in groundwater and provides promise for adsorbing and oxidizing a wide range of micropollutants, however, the continuous biodegradation and bioavailability of micropollutants via cycle biogenic Mn(II) oxidation remains to be elucidated. In this study, glyphosate was degraded and to serve as the nutrient source by a Pseudomonas sp. QJX-1. The addition of glyphosate will not affect the Mn(II) oxidation function of the strain but will affect its Mn(II) oxidation process and effect. The glyphosate degradation products could further be used as the C, N and P sources for bacterium growth. Analysis of the RNA-seq data suggested that Mn(II) oxidation driven by oxidoreductases for glyphosate degradation. The long-term column experiments using biological Mn(II) cycling to realize continuous detoxification and metabolism of glyphosate, and thus revealed the synergism effects of biological and chemical conversion on toxic micropollutants and continuous metabolism in an aquatic ecosystem.

Exposure of children to glyphosate in Morocco: Urinary levels and predictors of exposure

Glyphosate is one of the most frequently used organophosphorus plant protection products worldwide, and has recently been classified as probably carcinogenic to humans by the International Agency for Research and Cancer (IARC). We aimed to evaluate the urinary levels of glyphosate and its metabolite aminomethylphosphonic acid (AMPA) in Moroccan children, to identify the main predictors and to perform a risk assessment. Data was collected during a cross sectional study of 48 children from an intensive agricultural area. Measurements included a questionnaire on life-style, socio-demographic and herbicide exposures. Urinary glyphosate and AMPA were extracted using solid phase extraction (SPE) and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Overall, glyphosate and AMPA were detected in 73% and 75% of urine samples, respectively. The mean concentrations were 0.97 μg L^-1 (2.06 μg/g_creatinine) for glyphosate and 0.79 μg L^-1 (1.52 μg/g_creatinine) for AMPA. Children younger than 5 years had a higher AMPA and glyphosate urine concentration (mean = 2.24 μg L^-1; estimation coefficient (EC) = 1.39; 95% CI: 0.54-2.24) (mean = 4.05 μg L^-1; EC = 2.92; 95% CI: 1.68-4.15), respectively, than children aged 6-12. Children living near the pesticide spraying fields (<50 m) had 14.91 μg L^-1 and 2.35 μg L^-1 more glyphosate and AMPA, respectively, than children living in urban counties (95% CI: 8.14-20.91 for glyphosate and 95% CI: 0.55-4.14 for AMPA). AMPA concentration varied significantly with the source of drinking water, AMPA was higher among children that used water from open water sources (mean = 1.49 μg L^-1; EC = 2.98; 95% CI/0.67-5.78) compared to those using water from closed water sources. There were also non-significant associations found, such as total household net income, current parental job description, and dietary intake. With the regard to the health risk assessment, estimated daily intake (EDIs), hazard quotient (HQs), and a hazard index (HI) were calculated. The GMs of EDI were 4.38 and 2.26 μg/kg of body weight BW/day for glyphosate and AMPA, respectively. The HQs were calculated considering 0.5 mg/kg BW/day as an acceptable daily intake (ADI), which EFSA has established as a health-based reference value for both analytes. The value obtained were lower than 1, and therefore, low health risk due to glyphosate and AMPA was expected for the target population under the study. This study provides further evidence on factors associated with glyphosate exposure, especially in developing countries.

Insights into the microbial degradation and resistance mechanisms of glyphosate

Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.

Microbial community composition and glyphosate degraders of two soils under the influence of temperature, total organic carbon and pH

Glyphosate can be degraded by soil microorganisms rapidly and is impacted by temperature and soil properties. Enhanced temperature and total organic carbon (TOC) as well as reduced pH increased the rate of 13C315N-glyphosate conversion to CO2 and biogenic non-extractable residues (bioNERs) in a Haplic Chernozem (Muskus et al., 2019) and in a Humic Cambisol (Muskus et al., 2020). To date; however, the combined effect of temperature and TOC or pH on microbial community composition and glyphosate degraders in these two soils has not been investigated. Phospholipid fatty acid [PLFA] biomarker analysis combined with 13C labeling was employed to investigate the effect of two soil properties (pH, TOC) and of three temperatures (10 °C, 20 °C, 30 °C) on soil microorganisms. Before incubation, the properties of a Haplic Chernozem and a Humic Cambisol were adjusted to obtain five treatments: (a) Control (Haplic Chernozem: 2.1% TOC and pH 6.6; Humic Cambisol: 3% TOC and pH 7.0), (b) 3% TOC (Haplic Chernozem) or 4% TOC (Humic Cambisol), (c) 4% TOC (Haplic Chernozem) or 5% TOC (Humic Cambisol), (d) pH 6.0 (Haplic Chernozem) or pH 6.5 (Humic Cambisol), and (e) pH 5.5 for both soils. All treatments were amended with 50 mg kg-1 glyphosate and incubated at 10 °C, 20 °C or 30 °C. We observed an increase in respiration, microbial biomass and glyphosate mineralization with incubation temperature. Although respiration and microbial biomass in the Humic Cambisol was higher, the microorganisms in the Haplic Chernozem were more active in glyphosate degradation. Increased TOC shifted the microbiome and the 13C-glyphosate degraders towards Gram-positive bacteria in both soils. However, the abundance of 13C-PLFAs indicative for the starvation of Gram-negative bacteria increased with increasing TOC or decreasing pH at higher temperatures. Gram-negative bacteria thus may have been involved in earlier stages of glyphosate degradation.

AMPA-15N - Synthesis and application as standard compound in traceable degradation studies of glyphosate

Stable isotope labeling of pollutants is a valuable tool to investigate their environmental transport and degradation. For the globally most frequently used herbicide glyphosate, such studies have, so far, been hampered by the absence of an analytical standard for its labeled metabolite AMPA-15N, which is formed during the degradation of all commercially available glyphosate isotopologues. Without such a standard, detection and quantitation of AMPA-15N, e.g. with LC-MS/MS, is not possible. Therefore, a synthetic pathway to AMPA-15N from benzamide-15N via the hemiaminal was developed. AMPA-15N was obtained in sufficient yield and purity to be used as a standard compound for LC-MS/MS analysis. Suitable MS-detection settings as well as a calibration using the internal standard (IS) approach were established for Fmoc-derivatized AMPA-15N. The use of different AMPA isotopologues as IS was complicated by the parallel formation of [M+H]+ and [M]+• AMPA-Fmoc precursor ions in ESI-positive mode, causing signal interferences between analyte and IS. We recommend the use of either AMPA-13C-15N, AMPA-13C-15N-D2 or a glyphosate isotopologue as IS, as they do not affect the linearity of the calibration curve. As a proof of concept, the developed analysis procedure for AMPA-15N was used to refine the results from a field lysimeter experiment investigating leaching and degradation of glyphosate-2-13C-15N. The newly enabled quantitation of AMPA-15N in soil extracts showed that similar amounts (0.05 - 0.22 mg·kg-1) of the parent herbicide glyphosate and its primary metabolite AMPA persisted in the topsoil over the study period of one year, while vertical transport through the soil column did not occur for either of the compounds. The herein developed analysis concepts will facilitate future design and execution of experiments on the environmental fate of the herbicide glyphosate.

Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment

Agricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with agricultural stressors, we exposed freshwater mesocosms to single and combined gradients of two commonly used pesticides: the herbicide glyphosate (0-15 mg/L) and the neonicotinoid insecticide imidacloprid (0-60 μg/L), in high or low nutrient backgrounds. Over the 43-day experiment, we tracked variation in bacterial density with flow cytometry, carbon substrate use with Biolog EcoPlates, and taxonomic diversity and composition with environmental 16S rRNA gene amplicon sequencing. We show that only glyphosate (at the highest dose, 15 mg/L), but not imidacloprid, nutrients, or their interactions measurably changed community structure, favouring members of the Proteobacteria including the genus Agrobacterium. However, no change in carbon substrate use was detected throughout, suggesting functional redundancy despite taxonomic changes. We further show that communities are resilient at broad, but not fine taxonomic levels: 24 days after glyphosate application the precise amplicon sequence variants do not return, and tend to be replaced by phylogenetically close taxa. We conclude that high doses of glyphosate - but still within commonly acceptable regulatory guidelines - alter freshwater bacterioplankton by favouring a subset of higher taxonomic units (i.e., genus to phylum) that transiently thrive in the presence of glyphosate. Longer-term impacts of glyphosate at finer taxonomic resolution merit further investigation.

Molecular mechanisms underlying glyphosate resistance in bacteria

Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.

Pesticides in a case study on no-tillage farming systems and surrounding forest patches in Brazil

With the growing global concern on pesticide management, the relationship between its environmental recalcitrance, food security and human health has never been more relevant. Pesticides residues are known to cause significant environmental contamination. Here, we present a case study on long-term no-tillage farming systems in Brazil, where Glyphosate (GLY) has been applied for more than 35 years. GLY and its main breakdown product, aminomethylphosphonic acid (AMPA) were determined in topsoil (0-10 cm) samples from no-tillage fields and nearby subtropical secondary forests by high-performance liquid chromatography coupled with a fluorescence detector. In addition, the presence of carbamates, organochlorines, organophosphates and triazines were also screened for. GLY and AMPA were present in all soil samples, reaching values higher than those described for soils so far in the literature. A significant decrease for AMPA was observed only between the secondary forest and the farm's middle slope for site B. GLY and AMPA were observed respectively at peak concentrations of 66.38 and 26.03 mg/kg soil. GLY was strongly associated with forest soil properties, while AMPA associated more with no-tillage soil properties. Soil texture was a significant factor contributing to discrimination of the results as clay and sand contents affect GLY and AMPA retention in soils. This was the first study to report DDT and metabolites in consolidated no-tillage soils in Brazil (a pesticide fully banned since 2009). Based on human risk assessment conducted herein and the potential risk of GLY to local soil communities, this study offers a baseline for future studies on potential adverse effects on soil biota, and mechanistic studies.

The Challenge of Combining High Yields with Environmentally Friendly Bioproducts: A Review on the Compatibility of Pesticides with Microbial Inoculants

Inoculants or biofertilizers aiming to partially or fully replace chemical fertilizers are becoming increasingly important in agriculture, as there is a global perception of the need to increase sustainability. In this review, we discuss some important results of inoculation of a variety of crops with rhizobia and other plant growth-promoting bacteria (PGPB). Important improvements in the quality of the inoculants and on the release of new strains and formulations have been achieved. However, agriculture will continue to demand chemical pesticides, and their low compatibility with inoculants, especially when applied to seeds, represents a major limitation to the success of inoculation. The differences in the compatibility between pesticides and inoculants depend on their active principle, formulation, time of application, and period of contact with living microorganisms; however, in general they have a high impact on cell survival and metabolism, affecting the microbial contribution to plant growth. New strategies to solve the incompatibility between pesticides and inoculants are needed, as those that have been proposed to date are still very modest in terms of demand.

The carbon stable isotope compositions of glyphosate and aminomethylphosphonic acid (AMPA): Improved analytical sensitivity and first application to environmental water matrices

RATIONALE

The presence of glyphosate and its degradation product aminomethylphosphonic acid (AMPA) in the environment has adverse effects on environmental quality, raising the need to better constrain their fates, in particular the processes that control their production and degradation. Our aim was to improve the sensitivity of their δ¹³ C analysis and demonstrate the feasibility of measuring them in natural surface water.

METHODS

The δ¹³ C values of dissolved glyphosate and AMPA were determined using isotope ratio mass spectrometry (IRMS) (Delta V Plus instrument) coupled to a high-performance liquid chromatography (HPLC) unit, where glyphosate and AMPA were separated on a Hypercarb column.

RESULTS

We demonstrated an improved sensitivity of the δ¹³ C analysis for glyphosate and AMPA by LC/IRMS compared with previous studies. For waters from the carbonate and silicate hydrofacies, while no pretreatment was required for the isotope analysis of glyphosate, removal by H₃ PO₄ acidification of dissolved inorganic carbon, that co-elutes with AMPA, was required prior to its analysis. We successfully tested a freeze-drying pre-concentration method showing no associated isotope fractionation up to concentration factors of 500 and 50 for glyphosate and AMPA, respectively.

CONCLUSIONS

We demonstrated, for the first time, the feasibility of measuring the δ¹³ C values of glyphosate and AMPA in natural surface waters with contrasted hydrofacies (calcium carbonate and silicate types). This opens new fields in pesticide research, especially on the characterization of processes that control their degradation and the production of their secondary byproducts.

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

Evolution of Glyphosate-Resistant Weeds

Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

BACKGROUND

Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes.

RESULTS

We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the "Reactome," we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling.

CONCLUSIONS

Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services. Video Abstract.

Treatment technologies and degradation pathways of glyphosate: A critical review

Glyphosate is one of the most widely used post-emergence broad-spectrum herbicides in the world. This molecule has been frequently detected in aqueous environment and can cause adverse effects to plants, animals, microorganisms, and humans. This review offers a comparative assessment of current treatment methods (physical, biological, and advanced oxidation process) for glyphosate wastewaters, considering their advantages and drawbacks. As for other molecules, adsorption does not destroy glyphosate. It can be used before other processes, if glyphosate concentrations are very high, or after, to decrease the final concentration of glyphosate and its by-products. Most of biological and oxidation processes can destroy glyphosate molecules, leading to by-products (the main ones being AMAP and sarcosine) that can be or not affected by these processes. This point is of major importance to control process efficiency. That is the reason why a specific focus on glyphosate degradation pathways by biological treatment or different advanced oxidation processes is proposed. However, one process is usually not efficient enough to reach the required standards. Therefore, the combination of processes (for instance biological and oxidation ones) seems to be high-performance technologies for the treatment of glyphosate-containing wastewater, due to their potential to overcome some drawbacks of each individual process. Finally, this review provides indications for future work for different treatment processes to increase their performances and gives some insights into the treatment of glyphosate or other organic contaminants in wastewater.

Herbicide Glyphosate: Toxicity and Microbial Degradation

Glyphosate is a non-specific organophosphate pesticide, which finds widespread application in shielding crops against the weeds. Its high solubility in hydrophilic solvents, especially water and high mobility allows the rapid leaching of the glyphosate into the soil leading to contamination of groundwater and accumulation into the plant tissues, therefore intricating the elimination of the herbicides. Despite the widespread application, only a few percentages of the total applied glyphosate serve the actual purpose, dispensing the rest in the environment, thus resulting in reduced crop yields, low quality agricultural products, deteriorating soil fertility, contributing to water pollution, and consequently threatening human and animal life. This review gives an insight into the toxicological effects of the herbicide glyphosate and current approaches to track and identify trace amounts of this agrochemical along with its biodegradability and possible remediating strategies. Efforts have also been made to summarize the biodegradation mechanisms and catabolic enzymes involved in glyphosate metabolism.

Bacillus aryabhattai FACU: A promising bacterial strain capable of manipulate the glyphosate herbicide residues

Glyphosate is a commonly used organophosphate herbicide that has an adverse impact on humans, mammals and soil microbial ecosystems. The redundant utilize of glyphosate to control weed growth cause the pollution of the soil environment by this chemical. The discharge of glyphosate in the agricultural drainage can also cause serious environmental damage and water pollution problems. Therefore, it is important to develop methods for enhancing glyphosate degradation in the soil through bioremediation. In this study, thirty bacterial isolates were selected from an agro-industrial zone located in Sadat City of Monufia Governorate, Egypt. The isolates were able to grow in LB medium supplemented with 7.2 mg/ml glyphosate. Ten isolates only had the ability to grow in a medium containing different concentrations of glyphosate (50, 100, 150, 200 and 250 mg/ml). The FACU3 bacterial isolate showed the highest CFU in the different concentrations of glyphosate. The FACU3 isolate was Gram-positive, spore-forming and rod-shape bacteria. Based on API 50 CHB/E medium kit, biochemical properties and 16S rRNA gene sequencing, the FACU3 isolate was identified as Bacillus aryabhattai. Different bioinformatics tools, including multiple sequence alignment (MSA), basic local alignment search tool (BLAST) and primer alignment, were used to design specific primers for goxB gene amplification and isolation. The goxB gene encodes FAD-dependent glyphosate oxidase enzyme that responsible for biodegradation process. The selected primers were successfully used to amplify the goxB gene from Bacillus aryabhattai FACU3. The results indicated that the Bacillus aryabhattai FACU3 can be utilized in glyphosate-contaminated environments for bioremediation. According to our knowledge, this is the first time to isolate of FAD-dependent glyphosate oxidase (goxB) gene from Bacillus aryabhattai.

Differences of the microbial community structures and predicted metabolic potentials in the lake, river, and wetland sediments in Dongping Lake Basin

In freshwater ecosystems, wetlands are generally distinguished from deep-water ecosystems by 2-m water level as boundary. However, the difference of sediment microbial communities between wetlands and deep-water ecosystems is still unclear. We combined 16S rRNA gene sequencing and community metabolic prediction to compare sediment microbial communities and predicted metabolic genes of wetlands (natural and constructed wetlands) and deep-water ecosystems (river and lake) along with environmental factors in summer and autumn in Dongping Lake Basin. Results showed that the deep-water ecosystems had significantly higher community richness than the wetlands in autumn in the freshwater basin, which was mostly related to the pH of sediments. However, no significant difference in community richness was found in summer. Besides, the composition of both predicted metabolic genes and microbial communities was significantly affected by dissolved organic carbon (DOC) and dissolved oxygen (DO). The wetlands exhibited high predicted gene abundances related to xenobiotic biodegradation possibly due to the high DOC or DO level. Compared with the wetlands, most of the deep-water ecosystems exhibited high predicted gene abundances related to element (carbon, nitrogen, and sulfur) metabolism possibly due to the low DOC and DO levels in the freshwater basin. This study can expand the knowledge of ecological function distribution and detoxification mechanism of microbial communities in freshwater ecosystems.

Agnes Rimando, a Pioneer in the Fate of Glyphosate and Its Primary Metabolite in Plants

Glyphosate is the most used herbicide on the planet because of its excellent efficacy on almost all weed species and due to the large-scale adoption of transgenic, glyphosate-resistant (GR) crops. Agnes Rimando became an expert in glyphosate analysis almost 20 years ago to support research on GR crop safety and on mechanisms of evolved glyphosate resistance by weeds. Her work was the first to show that the amount of glyphosate and its primary metabolite aminomethylphosphonic acid (AMPA) that accumulates in GR soybean seed from plants treated with approved glyphosate doses can approach their legal limits. However, she later found that only trace amounts of these compounds accumulate in the seed of GR maize treated with recommended glyphosate doses. She showed that GR canola, the only transgenic crop with a transgene encoding an enzyme for degradation of glyphosate, metabolizes glyphosate to AMPA very rapidly. Her work was instrumental in providing support for the view that "yellow flash" symptoms sometimes observed in field-grown GR soybeans are due to accumulation of enough AMPA to cause mild phytotoxicity. She did the chemical analyses in the only paper to survey the capacity of an array of plant species to metabolize glyphosate to AMPA. She found a wide range in this capacity, with grasses with little or no metabolism of glyphosate to AMPA and with legumes readily metabolizing glyphosate. Lastly, she found no evidence of enhanced degradation of glyphosate to be a mechanism of evolved resistance to glyphosate by two weed species but that it might be involved in natural tolerance to glyphosate of some weeds.

Carbon-Phosphorus Lyase-the State of the Art

Organophosphonates are molecules that contain a very chemically stable carbon-phosphorus (C-P) bond. Microorganisms can utilize phosphonates as potential source of crucial elements for their growth, as developed several pathways to metabolize these compounds. One among these pathways is catalyzed by C-P lyase complex, which has a broad substrate specifity; therefore, it has a wide application in degradation of herbicides deposited in the environment, such as glyphosate. This multi-enzyme system accurately recognized in Escherichia coli and genetic studies have demonstrated that it is encoded by phn operon containing 14 genes (phnC-phnP). The phn operon is a member of the Pho regulon induced by phosphate starvation. Ability to degradation of phosphonates is also found in other microorganisms, especially soil and marine bacteria, that have homologous genes to those in E. coli. Despite the existence of differences in structure and composition of phn gene cluster, each of these strains contains phnGHIJKLM genes necessary in the C-P bond cleavage mechanism. The review provides a detailed description and summary of achievements on the C-P lyase enzymatic pathway over the last 50 years.

N-phosphonomethylglycine utilization by the psychrotolerant yeast Solicoccozyma terricola M 3.1.4

Solicoccozyma terricola M 3.1.4., the yeast strain isolated from soil sample from blueberry cultivation in Miedzyrzec Podlaski in Poland, is capable to split of phosphorus to nitrogen and nitrogen to carbon bonds in N-phosphonomethylglycine (PMG, glyphosate). The biodegradation process proceeds in the phosphate-independent manner. It is the first example of a psychrotolerant yeast strain able to degrade PMG via CN bond cleavage accompanied by AMPA formation and not like in most microorganisms via CP bond disruption followed by the sarcosine pathway. Glyphosate oxidoreductase (GOX) type activity was detected in cell-free extracts prepared from S. terricola M 3.1.4. pregrown on 4 mM PMG as a sole phosphorus and nitrogen source in cultivation medium.

Glyphosate: Its Environmental Persistence and Impact on Crop Health and Nutrition

Glyphosate-based herbicide products are the most widely used broad-spectrum herbicides in the world for postemergent weed control. There are ever-increasing concerns that glyphosate, if not used judiciously, may cause adverse nontarget impacts in agroecosystems. The purpose of this brief review is to present and discuss the state of knowledge with respect to its persistence in the environment, possible effects on crop health, and impacts on crop nutrition.

Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide

Herbicides increase crop yields by allowing weed control and harvest management. Glyphosate is the most widely-used herbicide active ingredient, with $11 billion spent annually on glyphosate-containing products applied to >350 million hectares worldwide, using about 8.6 billion kg of glyphosate. The herbicidal effectiveness of glyphosate can depend upon the time of day of spraying. Here, we show that the plant circadian clock regulates the effectiveness of glyphosate. We identify a daily and circadian rhythm in the inhibition of plant development by glyphosate, due to interaction between glyphosate activity, the circadian oscillator and potentially auxin signalling. We identify that the circadian clock controls the timing and extent of glyphosate-induced plant cell death. Furthermore, the clock controls a rhythm in the minimum effective dose of glyphosate. We propose the concept of agricultural chronotherapy, similar in principle to chronotherapy in medical practice. Our findings provide a platform to refine agrochemical use and development, conferring future economic and environmental benefits.

Soybean-Nodulating Strains With Low Intrinsic Competitiveness for Nodulation, Good Symbiotic Performance, and Stress-Tolerance Isolated From Soybean-Cropped Soils in Argentina

Soybean is the most important oilseed in the world, cropped in 120–130 million hectares each year. The three most important soybean producers are Argentina, Brazil, and United States, where soybean crops are routinely inoculated with symbiotic N₂-fixing Bradyrhizobium spp. This extended inoculation gave rise to soybean-nodulating allochthonous populations (SNAPs) that compete against new inoculant for nodulation, thus impairing yield responses. Competitiveness depends on intrinsic factors contributed by genotype, extrinsic ones determined by growth and environmental conditions, and strain persistence in the soil. To assess these factors in Argentinean SNAPs, we studied 58 isolates from five sites of the main soybean cropping area. BOX-A1R DNA fingerprint distributed these isolates in 10 clades that paralleled the pHs of their original soils. By contrast, reference Bradyrhizobium spp. strains, including those used as soybean-inoculants, were confined to a single clade. More detailed characterization of a subset of 11 SNAP-isolates revealed that five were Bradyrhizobium japonicum, two Bradyrhizobium elkanii, two Rhizobium radiobacter (formerly Agrobacterium tumefaciens), one Bradyrhizobium diazoefficiens, and one Paenibacillus glycanilyticus-which did not nodulate when inoculated alone, and therefore was excluded from further characterization. The remaining subset of 10 SNAP-isolates was used for deeper characterization. All SNAP-isolates were aluminum- and heat-tolerant, and most of them were glyphosate-tolerant. Meanwhile, inoculant strains tested were sensitive to aluminum and glyphosate. In addition, all SNAP-isolates were motile to different degrees. Only three SNAP-isolates were deficient for N₂-fixation, and none was intrinsically more competitive than the inoculant strain. These results are in contrast to the general belief that rhizobia from soil populations evolved as intrinsically more competitive for nodulation and less N₂-fixing effective than inoculants strains. Shoot:root ratios, both as dry biomass and as total N, were highly correlated with leaf ureide contents, and therefore may be easy indicators of N₂-fixing performance, suggesting that highly effective N₂-fixing and well-adapted strains may be readily selected from SNAPs. In addition, intrinsic competitiveness of the inoculants strains seems already optimized against SNAP strains, and therefore our efforts to improve nodules occupation by inoculated strains should focus on the optimization of extrinsic competitiveness factors, such as inoculant formulation and inoculation technology.

Identification of the first glyphosate transporter by genomic adaptation

The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.

The different behaviors of glyphosate and AMPA in compost-amended soil

The broad-spectrum herbicide glyphosate is one of the most widely used pesticides. Both glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA), persist in waters; thus, their environmental fates are of interest. We investigated the influence of compost dose, sampling depth, moisture and saturated hydraulic conductivity (Ks) on the persistence of these substances. The amounts of AMPA quantified by triple quadrupole liquid chromatography-mass spectrometry (LC-QqQ-MS/MS) using isotopically labeled extraction standards were higher than those of glyphosate and differed among the samples. Both glyphosate and AMPA showed gradually decreasing concentrations with soil depth, and bootstrapped ANOVA showed significant differences between the contents of glyphosate and AMPA and their behavior related to different compost dosages and sampling depths. However, the compost dose alone did not cause significant differences among samples. Bayesian statistics revealed that the amounts of glyphosate and AMPA were both dependent on the sampling depth and compost dose, but differences were found when considering the physical factors of Ks and moisture. Glyphosate was influenced by moisture but not Ks, whereas AMPA was influenced by Ks but not moisture. Importantly, we found behavioral differences between glyphosate and its major metabolite, AMPA, related to the physical properties of Ks and moisture.

Soil microbial communities and glyphosate decay in soils with different herbicide application history

This study evaluates the glyphosate dissipation under field conditions in three types of soil, and aims to determine the importance of the following factors in the environmental persistence of herbicide: i) soil bacterial communities, ii) soil physicochemical properties, iii) previous exposure to the herbicide. A soil without previous record of GP application (P0) and two agricultural soils, with 5 and >10years of GP exposure (A5 and A10) were subjected to the application of glyphosate at doses of 3mg·kg-1. The concentration of GP and AMPA was determined over time and the dynamics of soil bacterial communities was evaluated using 16S ARN ribosomal gene amplicon-sequencing. The GP exposure history affected the rate but not the extent of GP biodegradation. The herbicide was degraded rapidly, but P0 soil showed a dissipation rate significantly lower than soils with agricultural history. In P0 soil, a significant increase in the relative abundance of Bacteroidetes was observed in response to herbicide application. More generally, all soils displayed shifts in bacterial community structure, which nevertheless could not be clearly associated to glyphosate dissipation, suggesting the presence of redundant bacteria populations of potential degraders. Yet the application of the herbicide prompted a partial disruption of the bacterial association network of unexposed soil. On the other hand, higher values of linear (Kd) and nonlinear (Kf) sorption coefficient in P0 point to the relevance of cation exchange capacity (CEC), clay and organic matter to the capacity of soil to adsorb the herbicide, suggesting that bioavailability was a key factor for the persistence of GP and AMPA. These results contribute to understand the relationship between bacterial taxa exposed to the herbicide, and the importance of soil properties as predictors of the possible rate of degradation and persistence of glyphosate in soil.

Recent advances in glyphosate biodegradation

Glyphosate has emerged as the most widespread herbicide to control annual and perennial weeds. Massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Different approaches such as adsorption, photocatalytic degradation, and microbial degradation have been studied to break down glyphosate in the environment. Among these, microbial degradation is the most effective and eco-friendly method. During its degradation, various microorganisms can use glyphosate as a sole source of phosphorus, carbon, and nitrogen. Major glyphosate degradation pathways and its metabolites have been frequently investigated, but the related enzymes and genes have been rarely studied. There are many reviews about the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid. However, there is lack of reviews on biodegradation and bioremediation of glyphosate. The aims of this review are to summarize the microbial degradation of glyphosate and discuss the potential of glyphosate-degrading microorganisms to bioremediate glyphosate-contaminated environments. This review will provide an instructive direction to apply glyphosate-degrading microorganisms in the environment for bioremediation.

Monitoring of glyphosate and AMPA in soil samples from two olive cultivation areas in Greece: aspects related to spray operators activities

The persistence of glyphosate and its primary metabolite AMPA (aminomethylphosphonic acid) was monitored in two areas in Southern Greece (Peza, Crete and Chora Trifilias, Peloponnese) with a known history of glyphosate use, and the levels of residues were linked to spray operators' activities in the respective areas. A total of 170 samples were collected and analysed from both areas during a 3-year monitoring study. A new method (Impact Assessment Procedure - IAP) designed to assess potential impacts to the environment caused by growers' activities, was utilised in the explanation of the results. The level of residues was compared to the predicted environmental concentrations in soil. The ratio of the measured concentrations to the predicted environmental concentrations (MCs/PECs) was > 1 in Chora the first 2 years of sampling and < 1 in the third year, whilst the MCs/PECs ratio was < 1 in Peza, throughout the whole monitoring period. The compliance to the instructions for best handling practices, which operators received during the monitoring period, was reflected in the amount of residues and the MCs/PECs ratio in the second and especially the third sampling year. Differences in the level of residues between areas as well as sampling sites of the same area were identified. AMPA persisted longer than the parent compound glyphosate in both areas.

Non-point source pollution of glyphosate and AMPA in a rural basin from the southeast Pampas, Argentina

We measured the occurrence and seasonal variations of glyphosate and its metabolite, aminomethylphosphonic acid (AMPA), in different environmental compartments within the limits of an agricultural basin. This topic is of high relevance since glyphosate is the most applied pesticide in agricultural systems worldwide. We were able to quantify the seasonal variations of glyphosate that result mainly from endo-drift inputs, that is, from direct spraying either onto genetically modified (GM) crops (i.e., soybean and maize) or onto weeds in no-till practices. We found that both glyphosate and AMPA accumulate in soil, but the metabolite accumulates to a greater extent due to its higher persistence. Knowing that glyphosate and AMPA were present in soils (> 93% of detection for both compounds), we aimed to study the dispersion to other environmental compartments (surface water, stream sediments, and groundwater), in order to establish the degree of non-point source pollution. Also, we assessed the relationship between the water-table depth and glyphosate and AMPA levels in groundwater. All of the studied compartments had variable levels of glyphosate and AMPA. The highest frequency of detections was found in the stream sediments samples (glyphosate 95%, AMPA 100%), followed by surface water (glyphosate 28%, AMPA 50%) and then groundwater (glyphosate 24%, AMPA 33%). Despite glyphosate being considered a molecule with low vertical mobility in soils, we found that its detection in groundwater was strongly associated with the month where glyphosate concentration in soil was the highest. However, we did not find a direct relation between groundwater table depth and glyphosate or AMPA detections. This is the first simultaneous study of glyphosate and AMPA seasonal variations in soil, groundwater, surface water, and sediments within a rural basin.

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture

Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.

Impacts of glyphosate-based herbicides on disease resistance and health of crops: a review

Based on experimental data from laboratory and field, numerous authors have raised concern that exposure to glyphosate-based herbicides (GBHs) may pre-dispose crops to damage by microbial pathogens. In this review, we distinguish and evaluate two principal pathways by which GBHs may affect the susceptibility of crops to disease: pathway 1-via disruptions to rhizosphere microbial ecology, and pathway 2-via restriction of nutrients to crops. We conclude that GBHs have the potential to undermine crop health in a number of ways, including: (i) impairment of the innate physiological defences of glyphosate-sensitive (GS) cultivars by interruption of the shikimic acid pathway; (ii) impairment of physiological disease defences has also been shown to occur in some glyphosate-resistant (GR) cultivars, despite their engineered resistance to glyphosate's primary mode of action; (iii) interference with rhizosphere microbial ecology (in particular, GBHs have the potential to enhance the population and/or virulence of some phytopathogenic microbial species in the crop rhizosphere); and finally, (iv) the as yet incompletely elucidated reduction in the uptake and utilisation of nutrient metals by crops. Future progress will best be achieved when growers, regulators and industry collaborate to develop products, practices and policies that minimise the use of herbicides as far as possible and maximise their effectiveness when used, while facilitating optimised food production and security.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti

The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms.

Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes.

IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms.

Author Video: An author video summary of this article is available.

Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp

Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.

High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria

Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656 bp genome of Enterobacter sp. Bisph2 consists in one chromosome and no detectable plasmid, has a 53.19% GC content and 78% of genes were assigned a putative function. The genome contains four prophages of which 3 regions are intact and no CRISPER was detected. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JXAF00000000.

Differential Growth Responses of Marine Phytoplankton to Herbicide Glyphosate

Glyphosate is a globally popular herbicide to kill weeds and its wide applications may lead to accumulation in coastal oceans as a source of phosphorus (P) nutrient or growth inhibitor of phytoplankton. We studied the physiological effects of glyphosate on fourteen species representing five major coastal phytoplankton phyla (haptophyta, bacillariophyta, dinoflagellata, raphidophyta, and chlorophyta). Based on growth responses to different concentrations of glyphosate under contrasting dissolved inorganic phosphorus (DIP) conditions, we found that phytoplankton species could be classified into five groups. Group I (Emiliania huxleyi, Skeletonema costatum, Phaeodactylum tricornutum) could utilize glyphosate as sole P-source to support growth in axenic culture, but in the presence of DIP, they were inhibited by both 36-μM and 360-μM glyphosate. Group II (Karenia mikimotoi, Prorocentrum minimum, Dunaliella tertiolecta, Symbiodinium sp., Heterosigma akashiwo and Alexandrium catenella) could not utilize glyphosate as sole P-source to support growth, and in the presence of DIP growth was not affected by 36-μM but inhibited by 360-μM glyphosate. Glyphosate consistently enhanced growth of Group III (Isochrysis galbana) and inhibited Group IV (Thalassiosira weissflogii, Thalassiosira pseudonana and Chattonella marina) regardless of DIP condition. Group V (Amphidinium carterae) exhibited no measurable response to glyphosate regardless of DIP condition. This grouping is not congruent with the phylogenetic relationships of the phytoplankton species suggesting functional differentiation driven by environmental pressure. We conclude that glyphosate could be used as P-source by some species while is toxic to some other species and yet has no effects on others. The observed differential effects suggest that the continued use of glyphosate and increasing concentration of this herbicide in the coastal waters will likely exert significant impact on coastal marine phytoplankton community structure.

Glyphosate-Resistant Parthenium hysterophorus in the Caribbean Islands: Non Target Site Resistance and Target Site Resistance in Relation to Resistance Levels

Glyphosate has been the most intensely herbicide used worldwide for decades, and continues to be a single tool for controlling weeds in woody crops. However, the adoption of this herbicide in a wide range of culture systems has led to the emergence of resistant weeds. Glyphosate has been widely used primarily on citrus in the Caribbean area, but a study of resistance in the Caribbean islands of Cuba and the Dominican Republic has never been carried out. Unfortunately, Parthenium hysterophorus has developed glyphosate-resistance in both islands, independently. The resistance level and mechanisms of different P. hysterophorus accessions (three collected in Cuba (Cu-R) and four collected in the Dominican Republic (Do-R) have been studied under greenhouse and laboratory conditions. In in vivo assays (glyphosate dose causing 50% reduction in above-ground vegetative biomass and survival), the resistance factor levels showed susceptible accessions (Cu-S ≥ Do-S), low-resistance accessions (Cu-R3 < Do-R4), medium-resistance accessions (Do-R3 < Cu-R2 < Do-R2) and high-resistance accessions (Do-R1 < Cu-R1). In addition, the resistance factor levels were similar to those found in the shikimic acid accumulation at 1000 μM of glyphosate (Cu-R1 ≥ Do-R1 > Do-R2 > Cu-R2 > Do-R3 > Do-R4 > Cu-R3 >> Cu-S ≥ Do-S). Glyphosate was degraded to aminomethylphosphonic acid, glyoxylate and sarcosine by >88% in resistant accessions except in Cu-R3 and Do-R4 resistant accessions (51.12 and 44.21, respectively), whereas a little glyphosate (<9.32%) was degraded in both susceptible accessions at 96 h after treatment. There were significant differences between P. hysterophorus accessions in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity enzyme with and without different glyphosate rates. The R accessions showed values of between 0.026 and 0.21 μmol μg^-1 TSP protein min^-1 basal EPSPS activity values with respect to the S (0.024 and 0.025) accessions. The same trend was found in the EPSPS enzyme activity treated with glyphosate, where a higher enzyme activity inhibition (glyphosate μM) corresponded to greater resistance levels in P. hysterophorus accessions. One amino acid substitution was found at position 106 in EPSPS, consisting of a proline to serine change in Cu-R1, Do-R1 Do-R2. The above-mentioned results indicate that high resistance values are determined by the number of defense mechanisms (target-site and non-target-site resistance) possessed by the different P. hysterophorus accessions, concurrently.

Bioremediation potential of glyphosate-degrading Pseudomonas spp. strains isolated from contaminated soil

Bacterial strains capable of utilizing glyphosate as the sole carbon source were isolated from contaminated soil by the enrichment culture method and identified based on partial 16S rRNA gene sequence analysis. Pseudomonas spp. strains GA07, GA09 and GC04 demonstrated the best degradation capabilities towards glyphosate and were used for the laboratory experiments of glyphosate bioremediation. Inoculating glyphosate-treated soil samples with these three strains resulted in a 2-3 times higher rate of glyphosate removal than that in non-inoculated soil. The degradation kinetics was found to follow a first-order model with regression values greater than 0.96. Cell numbers of the introduced bacteria decreased from 4.4 × 10(6) CFU/g to 3.4-6.7 × 10(5) CFU/g dry soil within 18 days of inoculation. Due to the intense degradation of glyphosate, the total dehydrogenase activity of the soil microbial community increased by 21.2-25.6%. Analysis of glyphosate degradation products in cell-free extracts showed that glyphosate breakdown in strain GA09 was catalyzed both by C-P lyase and glyphosate oxidoreductase. Strains GA07 and GC04 degraded glyphosate only via glyphosate oxidoreductase, but no further metabolite was detected. These results highlight the potential of the isolated bacteria to be used in the bioremediation of GP-contaminated soils.

Purification and characterization of carbon-phosphorus bond-cleavage enzyme from glyphosate degrading Pseudomonas putida T5

An inducible, carbon-phosphorus bond-cleavage enzyme was purified from cells of Pseudomonas putida T5 grown on N-phosphonomethyl glycine. The native enzyme had a molecular mass of approximately 70 kD and upon sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), yielded a homogeneous protein band with an apparent molecular mass of about 70 kD. Activity of purified enzyme was increased by 627-fold compared to the crude extract and showed pH and temperature optima of approximately 7 and 30°C, respectively. The purified enzyme had an apparent Km and Vmax of 3.7 mM and 6.8 mM/min, respectively, for its sole substrate N-phosphonomethyl glycine. The enzyme was inhibited by phenylmethylsulfonyl fluoride (PMSF), indicating the presence of serine at the active site. The enzyme was not inhibited by SDS, suggesting the absence of disulfide linkage in the enzyme. The enzyme was found to be inhibited by most of the metals studied except Mg(2+). Detergents studied also inhibited glyphosate acting as a carbon-phosphorus bond-cleavage enzyme. Thus initial characterization of the purified enzyme suggested that it could be used as a potential candidate for glyphosate bioremediation.

Glyphosate herbicide affects belowground interactions between earthworms and symbiotic mycorrhizal fungi in a model ecosystem

Herbicides containing glyphosate are widely used in agriculture and private gardens, however, surprisingly little is known on potential side effects on non-target soil organisms. In a greenhouse experiment with white clover we investigated, to what extent a globally-used glyphosate herbicide affects interactions between essential soil organisms such as earthworms and arbuscular mycorrhizal fungi (AMF). We found that herbicides significantly decreased root mycorrhization, soil AMF spore biomass, vesicles and propagules. Herbicide application and earthworms increased soil hyphal biomass and tended to reduce soil water infiltration after a simulated heavy rainfall. Herbicide application in interaction with AMF led to slightly heavier but less active earthworms. Leaching of glyphosate after a simulated rainfall was substantial and altered by earthworms and AMF. These sizeable changes provide impetus for more general attention to side-effects of glyphosate-based herbicides on key soil organisms and their associated ecosystem services.

Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase

After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses.

Carbon-14-glyphosate behavior in relationship to pedoclimatic conditions and crop sequence

The recognition of glyphosate [(-phosphonomethyl) glycine] behavioral patterns can be readily examined using a pedoclimatic gradient. In the present study, glyphosate adsorption-desorption and degradation were examined under different scenarios in relationship to soil properties and soil use applications. Three sites with varied pedoclimatic conditions and two crop sequences were selected. Adsorption-desorption and glyphosate distribution in mineralized, extractable, and nonextractable fractions were assessed under laboratory conditions. Glyphosate sorption was characterized by isotherms and glyphosate degradation using the distribution of C-glyphosate radioactivity among mineralized fractions, two extractable fractions (in water, ER1; in NHOH, ER2), and nonextractable fractions. Results showed sorption indices (distribution coefficient and Freundlich sorption coefficient : 13.4 ± 0.3-64.1 ± 0.9 L kg and 16.2-60.6, respectively), and hysteresis increased among soil sites associated with decreasing soil particle size <2 μm, soil organic matter, and other soil properties associated with soil granulometry. A multiple stepwise regression analysis was applied to estimate the relationship between values and soil properties. Cation exchange capacity, water field capacity, and Bray-1 P were the soil properties retained in the equation. Soils under continuous soybean [ (L.) Merr.] (monoculture) treatment exhibited reduced glyphosate adsorption and decreased hysteresis desorption relative to soils under rotation. To our knowledge, these results are the first to demonstrate that soils with identical properties exhibited different glyphosate retention capacities based on crop sequence. We propose possible explanations for this observation. Our results suggested that characterization of the variability in soil property gradients can serve to determine glyphosate behavioral patterns, which can establish a criterion for use in reducing potential environmental risks.