Distribution of glyphosate and methylphosphonate catabolism systems in soil bacteria Ochrobactrum anthropi and Achromobacter sp

Ability of mixed fungal cultures to remove glyphosate from soil microcosms under stressful conditions

Many herbicides used extensively to manage weeds and protect economically important crops contain glyphosate (GP) as their main ingredient, which contaminates ecosystems when it spreads from the soil into the surrounding environment. This study evaluated the ability of two fungal strains to remove GP at a microcosm scale. The strains, Aspergillus oryzae AM2 and Mucor circinelloides 166, were tested on their own and in mixed cultures. The microcosms were conditioned at 30 or 70% field capacity (FC), and contaminated with 5000 or 15,000 mg kg-1 GP. The native microbial communities played a crucial role in the dissipation of the herbicide. At the end of the incubation (60 days), they had achieved removal percentages above 95% in most treatments. The exceptions were the microcosms subjected to hydric stress (30% FC) and contaminated with 15,000 mg kg-1 GP, in which the co-cultures outperformed the native microbial species (≥ 80 vs 33% removal, respectively). An increase in AMPA (aminomethylphosphonic acid), the main metabolite of GP degradation, was usually detected after 60 days, which indicates that biodegradation may have been one of the main mechanisms involved in the removal of the herbicide. These results provide information about the potential of two mixed fungal cultures (containing species that are native to agricultural soils) to remove GP under stressful conditions.

Influence of organophosphonates as alternative P-sources on bacterial transformation of glyphosate

Glyphosate biotransformation under phosphorus (P)-limiting conditions has been demonstrated for numerous bacterial strains. However, besides glyphosate bacteria can utilize a broad spectrum of other biogenic and synthetic organophosphorus compounds (e.g., organophosphonates, OPs) as P-sources. The ubiquity of OPs in the environment reduces the likelihood that bacteria will encounter conditions where glyphosate is the only P-containing compound. To study the impact of co-existing OPs on the biotransformation of glyphosate, we conducted batch cultivation experiments with the bacterial strains Achromobacter insolitus strain Kg 19 (A. Kg 19) and Ochrobactrum pituitosum strain GPr1-13 (O. GPr1-13) in which glyphosate and an additional OP were simultaneously provided as P-sources. Experiments with glyphosate and one additional monophosphonate (aminomethylphosphonate (AMPA), 2-aminoethylphosphonate (AEP), or phenylphosphonate (PPA)) showed that glyphosate was the least preferred P-source. Furthermore, the repeated supply of excess AMPA or AEP hindered the biotransformation of glyphosate. For strain A. Kg 19, AEP and AMPA threshold concentrations above which no glyphosate transformation occurred were approximately 40 and 120 μM, respectively. Conversely, in the presence of a synthetic diphosphonate (iminodi(methylene phosphonate) (IDMP) or 1-hydroxyethane 1,1-diphosphonate (HEDP)), strain A. Kg 19 preferred glyphosate as P-source. While IDMP was transformed after the depletion of glyphosate, HEDP concentration remained constant throughout the experiment and its presence retarded both cell growth and transformation of glyphosate. In light of the ubiquitous presence of AMPA and other OPs in the environment, our findings indicate that the presence of OPs may compromise the biotransformation potential of glyphosate, leading to lower transformation rates than those reported in previous studies.

Draft genome sequence of glyphosate-degrading Ochrobactrum sp. strain GPK 3 (VKM B-2554D) isolated from agricultural soil

The genome of Ochrobactrum sp. isolated from agricultural soil polluted with the herbicide glyphosate is reported. The genome size is 5.48 Mb with an average G + C content of 56.3%. This genomic data could contribute to a better understanding of biochemistry and regulatory mechanisms of microbial degradation of glyphosate and 2-aminoethylphosphonic acid.

Cathodic poised potential stimulated the electron-sensitive C-P lyase pathway in glyphosate biodegradation

Glyphosate, the most widely used herbicide globally, is accumulating in the environment and poses significant potential eco- and bio-toxicity risks. While natural attenuation of glyphosate has been reported, the efficacy varies considerably and the dominant metabolite, aminomethylphosphonic acid (AMPA), is potentially more persistent and toxic. This study investigated the bioelectrochemical system (BES) for glyphosate degradation under anaerobic, reductive conditions. Atomistic simulations using density functional theory (DFT) predicted increased thermodynamic favorability for the non-dominant C-P lyase degradation pathway under external charge, which suppressed AMPA production. Experimental results confirmed that cathodic poised potential (-0.4 V vs. Ag/AgCl) enhanced glyphosate degradation (75 % in BES vs. ∼40 % in the control conditions after 37 days), and lowered the AMPA yield (0.52 mol AMPA yield per mol glyphosate removed in BES vs. 0.77-0.86 mol mol-1 in the control conditions). Geobacter lovleyi was likely the active species driving the C-P lyase pathway, as evidenced by the increase of its relative abundance, the upregulation of its extracellular electron transfer genes (most notably mtr) and the up-regulation of its phnJ and hcp genes (encoding C-P layse and hydroxylamine reductase respectively).

Hydrogen isotope labeling unravels origin of soil-bound organic contaminant residues in biodegradability testing

Biodegradability testing in soil helps to identify safe synthetic organic chemicals but is still obscured by the formation of soil-bound 'non-extractable' residues (NERs). Present-day methodologies using radiocarbon or stable (13C, 15N) isotope labeling cannot easily differentiate soil-bound parent chemicals or transformation products (xenoNERs) from harmless soil-bound biomolecules of microbial degraders (bioNERs). Hypothesizing a minimal retention of hydrogen in biomolecules, we here apply stable hydrogen isotope - deuterium (D) - labeling to unravel the origin of NERs. Soil biodegradation tests with D- and 13C-labeled 2,4-D, glyphosate and sulfamethoxazole reveal consistently lower proportions of applied D than 13C in total NERs and in amino acids, a quantitative biomarker for bioNERs. Soil-bound D thus mostly represents xenoNERs and not bioNERs, enabling an efficient quantification of xenoNERs by just measuring the total bound D. D or tritium (T) labeling could thus improve the value of biodegradability testing results for diverse organic chemicals forming soil-bound residues.

Disentangling the Regulatory Response of Agrobacterium tumefaciens CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors

Phosphonates (PHTs), organic compounds with a stable C-P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted Agrobacterium tumefaciens CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the phn gene cluster, encoding the C-P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the phnG promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25-50 μM range in various samples, including soil and water.

Persistence and pathway of glyphosate degradation in the coastal wetland soil of central Delaware

Glyphosate is a globally dominant herbicide. Here, we studied the degradation and microbial response to glyphosate application in a wetland soil in central Delaware for controlling invasive species (Phragmites australis). We applied a two-step solid-phase extraction method using molecularly imprinted polymers designed for the separation and enrichment of glyphosate and aminomethylphosphonic acid (AMPA) from soils before their analysis by ultra-high-performance liquid chromatography (UHPLC) and Q Exactive Orbitrap mass spectrometry methods. Our results showed that approximately 90 % of glyphosate degraded over 100 d after application, with AMPA being a minor (<10 %) product. Analysis of glyphosate-specific microbial genes to identify microbial response and function revealed that the expression of the phnJ gene, which codes C-P lyase enzyme, was consistently dominant over the gox gene, which codes glyphosate oxidoreductase enzyme, after glyphosate application. Both gene and concentration data independently suggested that C-P bond cleavage-which forms sarcosine or glycine-was the dominant degradation pathway. This is significant because AMPA, a more toxic product, is reported to be the preferred pathway of glyphosate degradation in other soil and natural environments. The degradation through a safer pathway is encouraging for minimizing the detrimental impacts of glyphosate on the environment.

Genomics and taxonomy of the glyphosate-degrading, copper-tolerant rhizospheric bacterium Achromobacter insolitus LCu2

A rhizosphere strain, Achromobacter insolitus LCu2, was isolated from alfalfa (Medicago sativa L.) roots. It was able to degrade of 50% glyphosate as the sole phosphorus source, and was found resistant to 10 mM copper (II) chloride, and 5 mM glyphosate-copper complexes. Inoculation of alfalfa seedlings and potato microplants with strain LCu2 promoted plant growth by 30-50%. In inoculated plants, the toxicity of the glyphosate-copper complexes to alfalfa seedlings was decreased, as compared with the noninoculated controls. The genome of A. insolitus LCu2 consisted of one circular chromosome (6,428,890 bp) and encoded 5843 protein genes and 76 RNA genes. Polyphasic taxonomic analysis showed that A. insolitus LCu2 was closely related to A. insolitus DSM23807T on the basis of the average nucleotide identity of the genomes of 22 type strains and the multilocus sequence analysis. Genome analysis revealed genes putatively responsible for (1) plant growth promotion (osmolyte, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase biosynthesis and auxin metabolism); (2) degradation of organophosphonates (glyphosate oxidoreductase and multiple phn clusters responsible for the transport, regulation and C-P lyase cleavage of phosphonates); and (3) tolerance to copper and other heavy metals, effected by the CopAB-CueO system, responsible for the oxidation of copper (I) in the periplasm, and by the efflux Cus system. The putative catabolic pathways involved in the breakdown of phosphonates are predicted. A. insolitus LCu2 is promising in the production of crops and the remediation of soils contaminated with organophosphonates and heavy metals.

Glyphosate-Induced Phosphonatase Operons in Soil Bacteria of the Genus Achromobacter

Achromobacter insolitus and Achromobacter aegrifaciens, bacterial degraders of the herbicide glyphosate, were found to induce phosphonatase (phosphonoacetaldehyde hydrolase, EC 3.11.1.1) when grown on minimal media with glyphosate as the sole source of phosphorus. The phosphonatases of the strains were purified to an electrophoretically homogeneous state and characterized. The enzymes differed in their kinetic characteristics and some other parameters from the previously described phosphonatases. The phosphonatase of A. insolitus was first revealed to separate into two stable forms, which had similar kinetic characteristics but interacted differently with affinity and ion-exchange resins. The genomes of the investigated bacteria were sequenced. The phosphonatase genes were identified, and their context was determined: the bacteria were shown to have gene clusters, which, besides the phosphonatase operon, included genes for LysR-type transcription activator (substrate sensor) and putative iron-containing oxygenase PhnHD homologous to monooxygenases PhnY and TmpB of marine organophosphonate degraders. Genes of 2-aminoethylphosphonate aminotransferase (PhnW, EC 2.6.1.37) were absent in the achromobacterial phosphonatase operons; instead, we revealed the presence of genes encoding the putative flavin oxidase HpnW. In silico simulation showed 1-hydroxy-2-aminoethylphosphonate to be the most likely substrate of the new monooxygenase, and a number of glycine derivatives structurally similar to glyphosate to be substrates of flavin oxidase.

Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1

Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. This study illustrates that widely used and structurally more complex aminophosphonates can be degraded by Ochrobactrum sp. BTU1 via the well-known degradation pathways but with different initial cleavage strategy compared to GS.

Effect of temperature on the degradation of glyphosate by Mn-oxide: Products and pathways of degradation

Glyphosate is the most commonly used herbicide in the United States. In the environment, glyphosate residues can either degrade into more toxic and persistent byproducts such as aminomethylphosphonic acid (AMPA) or environmentally benign species such as sarcosine or glycine. In this research, the birnessite-catalyzed degradation of glyphosate was studied under environmentally relevant temperatures (10-40 °C) using high-performance liquid chromatography, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and theoretical calculations. Our results show a temperature-dependent degradation pathway preference for AMPA and glycine production. The AMPA and glycine pathways are competitive at short reaction times, but the glycine pathway became increasingly preferred as reaction time and temperature increased. The measured free energy barriers are comparable for both the glycine and AMPA pathways (93.5 kJ mol-1 for glycine and 97.1 kJ mol-1 for AMPA); however, the entropic energy penalty for the AMPA pathway is significantly greater than the glycine pathway (-TΔS‡ = 26.2 and 42.8 kJ mol-1 for glycine and AMPA, respectively). These findings provide possible routes for biasing glyphosate degradation towards safer products, thus to decrease the overall environmental toxicity.

Recent technologies for glyphosate removal from aqueous environment: A critical review

The growing demand for food has led to an increase in the use of herbicides and pesticides over the years. One of the most widely used herbicides is glyphosate (GLY). It has been used extensively since 1974 for weed control and is currently classified by the World Health Organization (WHO) as a Group 2A substance, probably carcinogenic to humans. The industry and academia have some disagreements regarding GLY toxicity in humans and its effects on the environment. Even though this herbicide is not mentioned in the WHO water guidelines, some countries have decided to set maximum acceptable concentrations in tap water, while others have decided to ban its use in crop production completely. Researchers around the world have employed different technologies to remove or degrade GLY, mostly at the laboratory scale. Water treatment plants combine different technologies to remove it alongside other water pollutants, in some cases achieving acceptable removal efficiencies. Certainly, there are many challenges in upscaling purification technologies due to the costs and lack of factual information about their adverse effects. This review presents different technologies that have been used to remove GLY from water since 2012 to date, its detection and removal methods, challenges, and future perspectives.

Hormesis of glyphosate on ferulic acid metabolism and antifungal volatile production in rice root biocontrol endophyte Burkholderia cepacia LS-044

Glyphosate (GP, N-phosphonomethyl glycine) is one of the most popular organophosphate herbicides widely used in agricultural practices worldwide. There have been extensive reports on the biohazard attributes and hormetic impacts of GP on plant and animal systems. However, the effects of GP on plant growth-promoting microbes and its ecological relevance remain unknown. Here, we show that GP does exert a hormetic impact on Burkholderia cepacia LS-044, a rice (Oryza sativa ssp. japonica cv. Tainung 71) root endophytic isolate. We used increasing doses of ferulic acid (FA, 1-25 mM) and GP (0.5-5 mM) to test the growth and antifungal volatile production in LS-044 by electrochemical, liquid chromatographic, gas chromatographic and spectrophotometric means. GP treatment at a low dose (0.5 mM) increased FA utilization and significantly (P < 0.0001) enhanced antifungal volatile activity in LS-044. Although FA (1 mM) was rapidly utilized by LS-044, no chromatographically detectable utilization of GP was observed at tested doses (0.5-5 mM). LS-044 emitted predominant amounts of tropone in addition to moderate-to-minor amounts of diverse ketones and/or their derivatives (acetone, acetophenone, 2-butanone, 1-propanone, 1-(2-furanyl-ethanone, 1-phenyl-1-propanone and 1-(3-pyridinyl)-1-propanone), d-menthol, 2-methoxy-3-(1-methylethyl)-pyrazine, dimethyl disulfide, pyridine and ammonium carbamate when grown under GP supplement. GP hormesis on LS-044 induced phenotypic variations in O. sativa ssp. japonica cv. Tainan 11 as evident through seed germination assay. Genes involved in the transformation of FA, and a key gene encoding 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) with Gly-94 and Tyr-95 residues localized at active site most likely rendering EPSPS sensitivity to GP, were detected in LS-044. This is the first report on the GP hormesis influencing morphological and metabolic aspects including volatile emission in a biocontrol bacterium that could modulate rice plant phenotype.

Microbial activity, community composition and degraders in the glyphosate-spiked soil are driven by glycine formation

Widely-used glyphosate may produce aminomethylphosphonic acid (AMPA), glycine and sarcosine. To date, little is known about effects of these degradation products on soil microorganisms and their potential degraders. Here, we incubated a soil spiked either with 2-13C-glyphosate, 13C-AMPA, 13C3-sarcosine or 13C2-glycine for 75 days. Respiration (CO2 tot) and mineralization rates of the compound (13CO2) were estimated in addition to phospholipid fatty acids (PLFAstot and 13C-PLFAs) as biomarkers to identify four groups of microorganisms (Gram-negative & Gram-positive bacteria, actinobacteria, fungi). 16S/ITS rRNA amplicon sequencing was also conducted to identify the microbial community at the phylum and genus level. The CO2 tot and 13CO2 rates were highest on day 2 in all treatments, as follows: glycine (CO2 tot: 1.09 μmol g-1; 13CO2: 18 %) > sarcosine (CO2 tot: 0.89 μmol g-1; 13CO2: 8.5 %) > glyphosate (CO2 tot: 0.67 μmol g-1; 13CO2: 2.2 %) > AMPA (CO2 tot: 0.53 μmol g-1; 13CO2: 0.3 %). Both the PLFAstot and 13C-PLFAs were highest in glycine (PLFAstot: 0.054-0.047 μmol g-1; 13C-PLFAs: 0.2-0.4 %) and glyphosate (PLFAstot: 0.049-0.047 μmol g-1; 13C-PLFAs: 0.1-0.3 %) treatments compared to sarcosine and AMPA treatments. Gram negative bacteria were major microbial group of soil microbiome as well as primary degraders of all compounds. In contrast, Gram-positive bacteria, actinobacteria and fungi could have been consumers of primary degraders. Certain genera e.g. Gemmatimonas, Arenimonas and Massilia showed increased abundance in certain treatments indicating their potential involvement in biodegradation. Based on similar time-dependent microbial activity and shifts in abundances of (13C-)PLFAs and 16S rRNA genera, we deduced that glyphosate was mainly degraded to glycine, and presumably at elevated amounts. We reported for the first time that the glycine presumably altered microbial activity and community composition rather than glyphosate directly. Future studies should thus also consider the potential impacts of degradation products of the parent compound on soil microbiomes.

The Microbial Degradation of Natural and Anthropogenic Phosphonates

Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.

Novel standard biodegradation test for synthetic phosphonates

Determination of biodegradation of synthetic phosphonates such as aminotris(methylenephosphonic acid) (ATMP), ethylenediamine tetra(methylenephosphonic acid) (EDTMP), or diethylenetriamine penta(methylenephosphonic acid) (DTPMP) is a great challenge. Commonly, ready biodegradability of organic substances is assessed by OECD 301 standard tests. However, due to the chemical imbalance of carbon to phosphorus synthetic phosphonates do not promote microbial growth and, thus, limiting its biodegradation. Therefore, standard OECD test methods are not always reliable to predict the real biodegradability of phosphonates. In the presented study, we report the development of a standardized batch system suitable to synthetic phosphonates such as ATMP, EDTMP, DTPMP and others. The novel standard batch test is applicable with pure strains, activated sludge from different wastewater treatment plants (i.e., municipal and industrial), and with tap water as inoculum. We optimized the required calcium and magnesium exposure levels as well as the amount of the start inoculum biomass. We demonstrated that our test also allows to determine several parameters including ortho-phosphate (o-PO43-), total phosphorus (TP), ammonium (NH4+) and total organic carbon (TOC). In addition, also LC/MS analyses of cell-free medium is applicable for determining the mother compounds and metabolites. We applied our optimized standardized batch with selected phosphonates and evidenced that the chemical structure has a major influence of the microbial growth rates. Thus, our novel batch test overcomes drawbacks of the OECD 301 test series for determination of easy biodegradability for stoichiometric imbalanced organic compounds such as phosphonates.

Characterization of a New Pseudomonas Putida Strain Ch2, a Degrader of Toxic Anthropogenic Compounds Epsilon-Caprolactam and Glyphosate

In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate (GP) as a sole source of phosphorus. Analysis of the nucleotide sequence of the 16S rRNA gene of Ch2 revealed that the strain belongs to the species Pseudomonas putida. This strain grew in the mineral medium containing CAP in a concentration range of 0.5 to 5.0 g/L and utilized 6-aminohexanoic acid and adipic acid, which are the intermediate products of CAP catabolism. The ability of strain Ch2 to degrade CAP is determined by a conjugative megaplasmid that is 550 kb in size. When strain Ch2 is cultured in a mineral medium containing GP (500 mg/L), more intensive utilization of the herbicide occurs in the phase of active growth. In the phase of declining growth, there is an accumulation of aminomethylphosphonic acid, which indicates that the C-N bond is the first site cleaved during GP degradation (glyphosate oxidoreductase pathway). Culture growth in the presence of GP during the early step of its degradation is accompanied by unique substrate-dependent changes in the cytoplasm, including the formation of vesicles of cytoplasmic membrane consisting of specific electron-dense content. There is a debate about whether these membrane formations are analogous to metabolosomes, where the primary degradation of the herbicide can take place. The studied strain is notable for its ability to produce polyhydroxyalkanoates (PHAs) when grown in mineral medium containing GP. At the beginning of the stationary growth phase, it was shown that, the amount and size of PHA inclusions in the cells drastically increased; they filled almost the entire volume of cell cytoplasm. The obtained results show that the strain P. putida Ch2 can be successfully used for the PHAs’ production. Moreover, the ability of P. putida Ch2 to degrade CAP and GP determines the prospects of its application for the biological cleanup of CAP production wastes and in situ bioremediation of soil polluted with GP.

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.

Effects of Free or Immobilized Bacterium Stenotrophomonas acidaminiphila Y4B on Glyphosate Degradation Performance and Indigenous Microbial Community Structure

The overuse of glyphosate has resulted in serious environmental contamination. Thus, effective techniques to remove glyphosate from the environment are required. Herein, we isolated a novel strain Stenotrophomonas acidaminiphila Y4B, which completely degraded glyphosate and its major metabolite aminomethylphosphonic acid (AMPA). Y4B degraded glyphosate over a broad concentration range (50-800 mg L^-1), with a degradation efficiency of over 98% within 72 h (50 mg L^-1). Y4B degraded glyphosate via the AMPA pathway by cleaving the C-N bond, followed by degradation of AMPA and subsequent metabolism. Y4B demonstrated strong competitiveness and substantially accelerated the degradation of glyphosate in different soils, degrading 71.93 and 89.81% of glyphosate (400 mg kg^-1) within 5 days in sterile and nonsterile soils, respectively. The immobilized cells of Y4B were more efficient than their free cells and they displayed excellent biodegradation efficiency in a sediment-water system. Taken together, Y4B is an ideal degrader for the bioremediation of glyphosate-contaminated sites.

Influence of glyphosate and its metabolite aminomethylphosphonic acid on aquatic plants in different ecological niches

Glyphosate and its metabolite aminomethylphosphonic acid (AMPA) draw great concern due to their potential threat to aquatic ecosystems. The individual and combined effects of glyphosate and AMPA on aquatic plants in different ecological niches need to be explored. This study aimed to investigate the ecotoxicity of glyphosate and AMPA on the emergent macrophyte Acorus calamus, phytoplankton Chlorella vulgaris, and submerged macrophyte Vallisneria natans after their exposure to glyphosate and AMPA alone and to their mixture. Medium and low concentrations of glyphosate (≤ 0.5 mg L^-1) significantly inhibited the growth of V. natans and promoted the growth of C. vulgaris (P < 0.05) but had no significant effect on the growth of A. calamus (P > 0.05). AMPA (≤ 5.0 mg L^-1) did not significantly influence the relative growth rate (except C. vulgaris) or malonaldehyde levels but significantly altered the expression levels of chlorophyll-related genes and superoxide dismutase [Cu-Zn] genes in the aquatic plants examined. AMPA mainly affected the oxidative phosphorylation pathway in V. natans and not those in other two plants, indicating that V. natans was more sensitive to AMPA-induced oxidative damage. Moreover, antagonistic effects on plant growth were observed when plants were exposed to low concentrations of glyphosate + AMPA (≤ 0.1 + 0.1 mg L^-1). When the concentration of glyphosate + AMPA reached 0.5 + 0.5 and 5.0 + 5.0 mg L^-1, the growth of the submerged macrophyte was additively or synergistically inhibited, but the growth of the emergent macrophyte and phytoplankton was antagonistically inhibited. Our results indicated that both the individual and combined effects of glyphosate and AMPA might alter the vertical structure of shallow lakes and accelerate the conversion of shallow lakes from grass-based to algal-based lakes.

Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems

Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems.

IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.

Characterization of a novel glyphosate-degrading bacterial species, Chryseobacterium sp. Y16C, and evaluation of its effects on microbial communities in glyphosate-contaminated soil

Widespread use of the herbicide glyphosate in agriculture has resulted in serious environmental problems. Thus, environment-friendly technological solutions are urgently needed for the removal of residual glyphosate from soil. Here, we successfully isolated a novel bacterial strain, Chryseobacterium sp. Y16C, which efficiently degrades glyphosate and its main metabolite aminomethylphosphonic acid (AMPA). Strain Y16C was found to completely degrade glyphosate at 400 mg·L-1 concentration within four days. Kinetics analysis indicated that glyphosate biodegradation was concentration-dependent, with a maximum specific degradation rate, half-saturation constant, and inhibition constant of 0.91459 d-1, 15.79796 mg·L-1, and 290.28133 mg·L-1, respectively. AMPA was identified as the major degradation product of glyphosate degradation, suggesting that glyphosate was first degraded via cleavage of its C-N bond prior to subsequent metabolic degradation. Strain Y16C was also found to tolerate and degrade AMPA at concentrations up to 800 mg·L-1. Moreover, strain Y16C accelerated glyphosate degradation in soil indirectly by inducing a slight alteration in the diversity and composition of soil microbial community. Taken together, our results suggest that strain Y16C may be a potential microbial agent for bioremediation of glyphosate-contaminated soil.

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.

Glyphosate Pollution Treatment and Microbial Degradation Alternatives, a Review

Glyphosate is a broad-spectrum herbicide extensively used worldwide to eliminate weeds in agricultural areas. Since its market introduction in the 70's, the levels of glyphosate agricultural use have increased, mainly due to the introduction of glyphosate-resistant transgenic crops in the 90's. Glyphosate presence in the environment causes pollution, and recent findings have proposed that glyphosate exposure causes adverse effects in different organisms, including humans. In 2015, glyphosate was classified as a probable carcinogen chemical, and several other human health effects have been documented since. Environmental pollution and human health threats derived from glyphosate intensive use require the development of alternatives for its elimination and proper treatment. Bioremediation has been proposed as a suitable alternative for the treatment of glyphosate-related pollution, and several microorganisms have great potential for the biodegradation of this herbicide. The present review highlights the environmental and human health impacts related to glyphosate pollution, the proposed alternatives for its elimination through physicochemical and biological approaches, and recent studies related to glyphosate biodegradation by bacteria and fungi are also reviewed. Microbial remediation strategies have great potential for glyphosate elimination, however, additional studies are needed to characterize the mechanisms employed by the microorganisms to counteract the adverse effects generated by the glyphosate exposure.

Glyphosate-degrading behavior of five bacterial strains isolated from stream biofilms

The present study investigates the individual degrading behavior of bacterial strains isolated from glyphosate-degrading stream biofilms. In this aim, biofilms were subjected to enrichment experiments using glyphosate or its metabolite AMPA (aminomethyl phosphonic acid) as the sole phosphorus source. Five bacterial strains were isolated and taxonomically affiliated to Ensifer sp. CNII15, Acidovorax sp. CNI26, Agrobacterium tumefaciens CNI28, Novosphingobium sp. CNI35 and Ochrobactrum pituitosum CNI52. All strains were capable of completely dissipating glyphosate after 125-400 h and AMPA after 30-120 h, except for Ensifer sp. CNII15 that was not able to dissipate glyphosate but entirely dissipated AMPA after 200 h. AMPA dissipation was overall faster than glyphosate dissipation. The five strains degraded AMPA completely since formaldehyde and/or glycine accumulation was observed. During glyphosate degradation, the strain CNI26 used the C-P lyase degradation pathway since sarcosine was quantitatively produced, and C-P lyase gene expression was enhanced 30× compared to the control treatment. However, strains CNI28, CNI35 and CNI52 accumulated both formaldehyde and glycine after glyphosate transformation suggesting that both C-P lyase and/or glyphosate oxidase degradation pathways took place. Our study shows different and complementary glyphosate degradation pathways for bacteria co-existing in stream biofilms.

Amazonian soil fungi are efficient degraders of glyphosate herbicide; novel isolates of Penicillium, Aspergillus, and Trichoderma

Pesticide residues that contaminate the environment circulate within the hydrological cycle can accumulate within the food chain and cause problems to both environmental and human health. Microbes, however, are well known for their metabolic versatility and the ability to degrade chemically stable substances, including recalcitrant xenobiotics. The current study focused on bio-prospecting within Amazonian rainforest soils to find novel strains fungi capable of efficiently degrading the agriculturally and environmentally ubiquitous herbicide, glyphosate. Of 50 fungal strains isolated (using culture media supplemented with glyphosate as the sole carbon-substrate), the majority were Penicillium strains (60%) and the others were Aspergillus and Trichoderma strains (26 and 8%, respectively). All 50 fungal isolates could use glyphosate as a phosphorous source. Eight of these isolates grew better on glyphosate-supplemented media than on regular Czapek Dox medium. LC-MS revealed that glyphosate degradation by Penicillium 4A21 resulted in sarcosine and aminomethylphosphonic acid.

Bacterial isolates from Argentine Pampas and their ability to degrade glyphosate

Glyphosate is a synthetic phosphonate compound characterized by a carbon‑phosphorus bond. Glyphosate based herbicides (GBH) are widely distributed in most of the economically productive lands in which crop production is mainly based on glyphosate-resistant genetically modified plants. Naturally, glyphosate is remediated by soil microorganisms, which accelerate its degradation. Technology based on microorganisms is considered highly efficient, low-cost and eco-friendly to remediate contaminated environments, denoting the importance of characterizing new bacterial strains able to degrade glyphosate to perform its bioremediation. In this work, 13 different bacterial strains able to grow in GBH as only phosphorous source were isolated from different environmental samples from the Argentine vastly productive glyphosate-resistant soybean crop area. These strains were identified and they belong to the genera Acinetobacter, Achromobacter, Agrobacterium, Ochrobactrum, Pantoea and Pseudomonas. Their ability to grow and consume GBH, glyphosate or the aminomethylphosphonic acid (AMPA), another phosphonate derived from glyphosate degradation, was evaluated. The best degradation performance was observed for bacteria from the genera Achromobacter, Agrobacterium and Ochrobactrum. The genome of the highly efficient GBH degrader Agrobacterium tumefaciens CHLDO was sequenced revealing the presence of a phn cluster, responsible for phosphonate metabolization. Expression analysis of A. tumefaciens CHLDO phn genes in the presence of 1.5 mM GBH compared to inorganic phosphorous showed that most of them are highly expressed during growth in the presence of the herbicide, suggesting a strong participation of phn cluster in GBH degradation. The importance of discovering new bacterial strains and the value of deciphering molecular determinants of GBH degradation give promising tools for bioremediation techniques to be used in glyphosate-contaminated environments is discussed.

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.

Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies

Widespread application of glyphosate poses a threat to living organisms. Microbial strains are able to degrade glyphosate via contrasting metabolic pathways with the help of enzymes. Glyphosate oxidoreductase (GOX) and C-P lyase are the key enzymes for the biodegradation of glyphosate and its intermediate metabolite aminomethylphosphonic acid (AMPA) in microbes. The microbial degradation of glyphosate has been reported, but the underlying molecular mechanism is still unclear. Therefore, in this study, the interaction mechanism of GOX and C-P lyase with glyphosate and AMPA were investigated by using molecular docking and molecular dynamics (MD) simulations. The results indicate that glyphosate contacts with the active site of GOX and C-P lyase by hydrogen bonds as well as hydrophobic and van der Waals interactions in aqueous solution to maintain its stability. The presence of glyphosate and AMPA in the active site significantly changes the conformation of GOX and C-P lyase. The results of the MD simulations confirm that GOX and C-P lyase complexes are stable during the catalytic reaction. This study offers a molecular level of understanding of the expression and function of GOX and C-P lyase for the bioremediation of glyphosate.

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.

Interaction between glyphosate and dissolved phosphorus on bacterial and eukaryotic communities from river biofilms

Since the capacity of river biofilms to degrade glyphosate has been proven to increase when the availability of dissolved phosphorus (P) in water decreases, the present study investigates the diversity responses of bacterial and eukaryotic microbial communities from biofilms in a search for glyphosate-degrader candidates. Glyphosate and P interactions were observed for eukaryotic communities, the highest community richness and diversity being preserved at low concentrations of glyphosate and P. This trend marked by glyphosate was also observed in the structure of eukaryotic communities. Therefore, phosphorus and glyphosate had a synergistic effect in decreasing the richness and diversity of eukaryotes species in biofilms. However, species richness and diversity in bacterial communities were not affected by glyphosate, though shifts in the structure of these communities were concomitant with the degradation of the herbicide. Bacterial communities capable of using glyphosate as P source were characterized by increases in the relative abundance of certain Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes and alpha-Proteobacteria members. Glyphosate-degrader candidates found in natural river biofilms can be further isolated for better understanding of glyphosate degradation pathways, and used as bioremediation strategies in heavily contaminated sites.

The Effects of Glyphosate and Its Commercial Formulations to Marine Invertebrates: A Review

Glyphosate is the active ingredient of numerous commercial formulations of herbicides applied in different sectors, from agriculture to aquaculture. Due to its widespread use around the world, relatively high concentrations of glyphosate have been detected in soil and aquatic environments. The presence of glyphosate in aquatic ecosystems has aroused the attention of researchers because of its potential negative effects on living organisms, both animals and plants. In this context, this review intends to summarize results of studies aimed at evaluating the effects of glyphosate (both as active ingredient and component of commercial formulations) on marine invertebrates. Generally, data obtained in acute toxicity tests indicate that glyphosate and its commercial formulations are lethal at high concentrations (not environmentally realistic), whereas results of long-lasting experiments indicate that glyphosate can markedly affect biological responses of marine invertebrates. Consequently, more efforts should be addressed at evaluating chronic or sub-chronic effects of such substances to marine invertebrate species.

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.

Primer design to assess bacterial degradation of glyphosate and other phosphonates

Phosphonates are organic phosphorous (P) compounds frequently detected in the environment due to a very stable CP bond that render them relatively recalcitrant. Glyphosate [N-phosphonomethyl glycine] is the most widely used and best-known synthetic phosphonate, and one of the most concerning herbicides in the world today. Microbial degradation of glyphosate and organophosphonates in general, is the main dissipation mechanism operating in most environments. One microbial metabolic pathway in this process is the CP lyase pathway, entailing an enzymatic complex encoded by about 14 genes (the Phn operon). Our goal was to develop a quantitative polymerase chain reaction (qPCR) assay for a key enzyme, the CP lyase that breaks down the CP bond, via quantification of the codifying phnJ gene. The primers designed in this study fulfill the requirements for a successful qPCR assay, with high efficiency and sensitivity, as well as specific detection of the target sequence in a wide range of taxonomic groups. This is, to our knowledge, the first report of primers designed to target phnJ in both pure cultures and metagenomic DNA from different environmental sources. Direct quantification of phnJ may be a cost-effective proxy to determine glyphosate degradation potential in different matrixes.

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.

Exploring the glyphosate-degrading characteristics of a newly isolated, highly adapted indigenous bacterial strain, Providencia rettgeri GDB 1

This study explored the characteristics of a newly isolated glyphosate (GLYP)-degrading bacterium Providencia rettgeri GDB 1, for GLYP bioremediation. Due to the serial selection pressure of high GLYP concentrations for enriched isolation, this highly tolerant GLYP biodegrader shows very promising capabilities for GLYP removal (approximately 71.4% degradation efficiency) compared to previously reported strains. High performance liquid chromatography analyses showed aminomethylphosphonic acid (AMPA) rather than sarcosine (SAR) to be the sole intermediate of GLYP decomposition via the AMPA formation pathway. Moreover, GLYP biodegradation was biochemically favorable in aerobic cultures due to its strong growth-associated characteristics. To the best of our knowledge, this is the first report to indicate that bacterial strains in the Providencia genus could demonstrate highly promising GLYP-degrading characteristics in environments with high GLYP contents.

Microbial Turnover of Glyphosate to Biomass: Utilization as Nutrient Source and Formation of AMPA and Biogenic NER in an OECD 308 Test

Environmental fate assessment of chemicals involves standardized simulation tests with isotope-labeled molecules to balance transformation, mineralization, and formation of nonextractable residues (NER). Methods to predict microbial turnover and biogenic NER have been developed, having limited use when metabolites accumulate, the chemicals are not the only C source, or provide for other macroelements. To improve predictive capability, we extended a recently developed method for microbial growth yield estimation to account for incomplete degradation and multiple-element assimilation and combined it with a dynamic model for fate description in soils and sediments. We evaluated the results against the unique experimental data of 13C3-15N co-labeled glyphosate turnover with AMPA formation in water-sediment systems (OECD 308). Balancing 13C- and 15N- fluxes to biomass showed a pronounced shift of glyphosate transformation from full mineralization to AMPA formation. This may be explained by various hypotheses, for example, the limited substrate turnover inherent to the batch conditions of the test system causing microbial starvation or inhibition by P release. Modeling results indicate initial N overload due to the lower C/N ratio in glyphosate compared to average cell composition leading to subsequent C demand and accumulation of AMPA.

Microcosm experiments and kinetic modeling of glyphosate biodegradation in soils and sediments

Glyphosate (GLP) is one of the most widely-used herbicides globally and its toxicity to humans and the environment is controversial. GLP is biodegradable, but little is known about the importance of site exposure history and other environmental variables on the rate and pathway of biodegradation. Here, GLP was added to microcosms of soils and sediments with different exposure histories and these were incubated with amendments of glucose, ammonium, and phosphate. GLP concentrations were measured with a newly-developed HPLC method capable of tolerating high concentrations of ammonium and amino acids. GLP biodegradation occurred after a lag-time proportional to the level of GLP pre-exposure in anthropogenically-impacted samples (soils and sediments), while no degradation occurred in samples from a pristine sediment after 180 days of incubation. Exposure history did not influence the rate of GLP degradation, after the lag-time was elapsed. Addition of C, N, and P triggered GLP degradation in pristine sediment and shortened the lag-time before degradation in other samples. In all microcosms, GLP was metabolised into aminomethylphosphonic acid (AMPA), which was highly persistent, and thus appears to be a more problematic pollutant than GLP. Bacterial communities changed along the gradients of anthropogenic impacts, but in some cases, taxonomically very-similar communities showed dramatically different activities with GLP. Our findings reveal important interactions between agriculturally-relevant nutrients and herbicides.

Ochrobactrum cytisi IPA7.2 promotes growth of potato microplants and is resistant to abiotic stress

Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain's potential to promote the growth of potato (Solanum tuberosum L.) microplants. Using the IPA7.2 draft genome (no. NZ_MOEC00000000), we searched for housekeeping genes and also for the target genes encoding glyphosate tolerance and plant-growth-promoting ability. A multilocus sequence analysis of the gap, rpoB, dnaK, trpE, aroC, and recA housekeeping genes led us to identify isolate IPA7.2 as O. cytisi. The strain tolerated temperatures up to 50 °C and NaCl concentrations up to 3-4%, and it produced 8 µg ml-1 of indole-3-acetic acid. It also tolerated 6 mM glyphosate owing to the presence of type II 5-enolpyruvylshikimate-3-phosphate synthase. Finally, it was able to colonize the roots and tissues of potato microplants, an ability preserved by several generations after subculturing. We identified the development phase of potato microplants that was optimal for inoculation with O. cytisi IPA7.2. Inoculation of in vitro-grown 15-day-old microplants increased the mitotic index of root meristem cells (by 50%), the length of shoots (by 34%), the number of leaves (by 7%), and the number of roots (by 16%). Under ex vitro conditions, the inoculated plants had a greater leaf area (by 77%) and greater shoot and root dry weight (by 84 and 61%, respectively) than did the control plants. We recommend O. cytisi IPA 7.2 for use in the growing of potato microplants to improve the production of elite seed material.

High Permeation Rates in Liposome Systems Explain Rapid Glyphosate Biodegradation Associated with Strong Isotope Fractionation

Bacterial uptake of charged organic pollutants such as the widely used herbicide glyphosate is typically attributed to active transporters, whereas passive membrane permeation as an uptake pathway is usually neglected. For 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) liposomes, the pH-dependent apparent membrane permeation coefficients ( Papp) of glyphosate, determined by nuclear magnetic resonance (NMR) spectroscopy, varied from Papp (pH 7.0) = 3.7 (±0.3) × 10-7 m·s-1 to Papp (pH 4.1) = 4.2 (±0.1) × 10-6 m·s-1. The magnitude of this surprisingly rapid membrane permeation depended on glyphosate speciation and was, at circumneutral pH, in the range of polar, noncharged molecules. These findings point to passive membrane permeation as a potential uptake pathway during glyphosate biodegradation. To test this hypothesis, a Gram-negative glyphosate degrader, Ochrobactrum sp. FrEM, was isolated from glyphosate-treated soil and glyphosate permeation rates inferred from the liposome model system were compared to bacterial degradation rates. Estimated maximum permeation rates were, indeed, 2 orders of magnitude higher than degradation rates of glyphosate. In addition, biodegradation of millimolar glyphosate concentrations gave rise to pronounced carbon isotope fractionation with an apparent kinetic isotope effect, AKIEcarbon, of 1.014 ± 0.003. This value lies in the range typical of non-masked enzymatic isotope fractionation demonstrating that glyphosate biodegradation was not subject to mass transfer limitations and glyphosate exchange across the cell membrane was rapid relative to enzymatic turnover.

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.

Degradation of Glyphosate by Mn-Oxide May Bypass Sarcosine and Form Glycine Directly after C-N Bond Cleavage

Glyphosate is the active ingredient of the common herbicide Roundup. The increasing presence of glyphosate and its byproducts has raised concerns about its potential impact on the environment and human health. In this research, we investigated abiotic pathways of glyphosate degradation as catalyzed by birnessite under aerobic and neutral pH conditions to determine whether certain pathways have the potential to generate less harmful intermediate products. Nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography (HPLC) were utilized to identify and quantify reaction products, and density functional theory (DFT) calculations were used to investigate the bond critical point (BCP) properties of the C-N bond in glyphosate and Mn(IV)-complexed glyphosate. We found that sarcosine, the commonly recognized precursor to glycine, was not present at detectable levels in any of our experiments despite the fact that its half-life (∼13.6 h) was greater than our sampling intervals. Abiotic degradation of glyphosate largely followed the glycine pathway rather than the AMPA (aminomethylphosphonic acid) pathway. Preferential cleavage of the phosphonate adjacent C-N bond to form glycine directly was also supported by our BCP analysis, which revealed that this C-N bond was disproportionately affected by the interaction of glyphosate with Mn(IV). Overall, these results provide useful insights into the potential pathways through which glyphosate may degrade via relatively benign intermediates.

Analysis of glyphosate degradation in a soil microcosm

Glyphosate (GLP) herbicide leaching into soil can undergo abiotic degradation and two enzymatic oxidative or hydrolytic reactions in both aerobic and anaerobic conditions; biotic oxidation produces aminomethylphosphonic acid (AMPA). Both GLP and AMPA are phytotoxic. A comprehensive GLP degradation reaction network was developed from the literature to account for the above pathways, and fifteen experimental data sets were used to determine the corresponding Michaelis-Menten-Monod (MMM) kinetic parameters. Various sensitivity analyses were designed to assess GLP and AMPA degradation potential against O2 (aq) and carbon (C) availability, pH, and birnessite mineral content, and showed that bacteria oxidized or hydrolyzed up to 98% of GLP and only 9% of AMPA. Lack of a C source limited the GLP cometabolic hydrolytic pathways, which produces non-toxic byproducts and promotes AMPA biodegradation. Low bacterial activity in O2 (aq)-limited conditions or non-neutral pH resulted in GLP accumulation. Birnessite mineral catalyzed fast GLP and AMPA chemodegradation reaching alone efficiencies of 79% and 88%, respectively, regardless of the other variables and produced non-toxic byproducts. Overall, O2 (aq) and birnessite availability played the major roles in determining the partitioning of GLP and its byproducts mass fluxes across the reaction network, while birnessite, C availability, and pH affected GLP and AMPA biodegradation effectiveness.

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.