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Systematic Review

Biodegradation Potential of Glyphosate by Bacteria: A Systematic Review on Metabolic Mechanisms and Application Strategies

by
Karolayne Silva Souza
1,*,
Milena Roberta Freire da Silva
1,
Manoella Almeida Candido
1,
Hévellin Talita Sousa Lins
1,
Gabriela de Lima Torres
2,
Kátia Cilene da Silva Felix
3,
Kaline Catiely Campos Silva
4,
Ricardo Marques Nogueira Filho
4,
Rahul Bhadouria
5,
Sachchidanand Tripathi
6,
Rishikesh Singh
7,
Milena Danda Vasconcelos Santos
1,
Isac Palmeira Santos Silva
3,
Amanda Vieira de Barros
1,
Lívia Caroline Alexandre de Araújo
1,
Fabricio Motteran
1 and
Maria Betânia Melo de Oliveira
1
1
Federal University of Pernambuco, Recife CEP 50740-540, Pernambuco, Brazil
2
Frassinetti University Center of Recife, Recife CEP 52011-210, Pernambuco, Brazil
3
Rio São Francisco University Center, Paulo Afonso CEP 48608-240, Bahia, Brazil
4
University of the State of Bahia, Paulo Afonso CEP 48609-000, Bahia, Brazil
5
Delhi College of Arts and Commerce, University of Delhi, Delhi 110023, India
6
Deen Dayal Upadhyay College, University of Delhi, Delhi 110078, India
7
Amity School of Earth & Environmental Sciences, Amity University Punjab, Mohali 140306, India
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(5), 1247; https://doi.org/10.3390/agronomy15051247
Submission received: 5 November 2024 / Revised: 16 December 2024 / Accepted: 22 December 2024 / Published: 21 May 2025
(This article belongs to the Section Weed Science and Weed Management)
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Versions Notes

Abstract

:
The biodegradation of glyphosate by bacteria is an emerging bioremediation strategy necessitated by the intensive use of this herbicide in global agriculture. This study systematically reviews the literature to identify bacteria with the potential to degrade glyphosate. The PRISMA protocol was utilized, considering relevant articles identified in electronic databases such as PubMed, Scopus, and Science Direct. The research identified 34 eligible studies, highlighting the genera Bacillus, Pseudomonas, and Ochrobactrum as having the greatest potential for glyphosate degradation. These findings were based on analytical techniques such as High-Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR), which identified and quantified intermediate metabolites, primarily AMPA (aminomethylphosphonic acid), sarcosine, and glyoxylate. This investigation also addressed enzymatic efficiency in biodegradation, emphasizing enzymes like glyphosate oxidoreductase and C-P lyases. The results indicated that South and North America lead in publications on this topic, with Argentina and the United States being the main contributors, reflecting the intense use of glyphosate in these countries. Additionally, studies in Europe and Asia focused on microbial diversity, exploring various bacterial genera. This investigation revealed that despite the promising microbial potential, there are challenges related to environmental condition variations and the cost of large-scale implementation, indicating that continuous research and process optimization are essential for the effective and sustainable application of this biotechnology.

1. Introduction

Glyphosate (N-phosphonomethylglycine) is a systemic, non-selective, and broad-spectrum herbicide developed in 1971 in the United States (USA). Due to its high physical and chemical stability, glyphosate is considered an effective and low-cost herbicide, widely used in agriculture, forestry, and livestock [1]. Currently, approximately 600,000 to 750,000 tons of glyphosate are used annually worldwide, and it is estimated that this number will increase from 740,000 to 920,000 tons by 2025 [2].
This herbicide inhibits the shikimic acid pathway, specifically in weeds (plants that grow spontaneously in undesirable locations and times, negatively impacting agriculture), thus blocking the production of 5-enolpyruvylshikimate-3-phosphate (EPSP). Consequently, this blockage prevents the production of aromatic amino acids such as tryptophan, tyrosine, and phenylalanine, resulting in the loss of green coloration in plants, leaf deformation, and eventually plant atrophy and death within 7–21 days of herbicide exposure [3].
Although glyphosate is considered safe, its uncontrolled use poses chronic risks to humans and the environment. According to the International Agency for Research on Cancer (IARC), glyphosate has been classified as “probably carcinogenic” to humans [4]. Consequently, environmental concerns regarding the use of pesticides and their metabolites have prompted the scientific community to investigate more effective degradation alternatives. Various physicochemical approaches, such as ultrasonic treatment, titanium dioxide photocatalysis, synthetic nanocomposites, and biochar adsorption, are used to detoxify xenobiotics, including pesticides. However, these methods, while rapid and efficient, produce highly toxic secondary metabolites, are expensive, and have limitations in degrading different xenobiotics [5,6].
Currently, one of the most viable alternatives to mitigate the environmental impacts caused by these pollutants is the biodegradation process. Recognized as a natural and effective remediation technique, biodegradation primarily utilizes microorganisms [7]. Microorganism-driven glyphosate degradation is considered a dominant strategy for soil decontamination in the 21st century, making it an attractive tool for recovering contaminated environments. To date, two main biodegradation pathways have been described: the glyphosate oxidase pathway (or AMPA—aminomethylphosphonic acid pathway) and the C-P lyase pathway (or sarcosine pathway) [8,9].
This study aims to explore the potential for glyphosate degradation by bacteria, which is based on the need to understand the metabolic mechanisms of these bacteria, including the enzymes involved and the metabolites generated. This allows for a more controlled and comparative analysis between different bacterial species, helping to identify the specific characteristics that make them effective in bioremediation. Thus, the main objective is to synthesize the available data to formulate practical guidelines for future biotechnological applications, focusing on the viability of these cultures in environmental remediation systems.

2. Methodology

Protocol

This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol [10], which is organized into the planning, execution, and data reporting phases.

3. Eligibility Criteria

To conduct this investigation, the PECO strategy [11] was adopted: Population: Microorganisms, Exposure: Glyphosate, Comparison: Not applicable, and Outcomes: Potential for Glyphosate Biodegradation by Bacteria. Based on this approach, studies that analyzed the main microorganisms involved in glyphosate biodegradation were considered eligible, without restrictions on the year of publication or language. Exclusion criteria included editorial studies, discussion papers, commentaries, letters, reviews, studies with incomplete or insufficient methodological data, duplicates, and titles not directly related to the proposed topic.

4. Information Sources and Search

Searches were conducted in the electronic databases and libraries of PubMed, Scopus, and Science Direct. Medical Subject Headings (MeSH) and Health Sciences Descriptors (DeCS), along with keywords and Boolean operators, were defined to formulate a controlled search strategy. The terms used were as follows: “Biodegradation, Environmental” AND “Glyphosate” AND “Herbicides” AND “Glyphosate Biodegradation” AND “Herbicide degradation” AND “Bioremediation.”

5. Article Selection

For the selection of studies, two reviewers independently and blindly followed the established inclusion and exclusion steps. In the first step, titles were analyzed, and duplicates were excluded. In the second step, eligibility criteria were individually discussed based on the PECO strategy, allowing for the exclusion of studies not aligned with the proposal. The third step involved reading the abstracts and eliminating those studies that did not provide sufficient information and data to meet the research objectives.

6. Data Collection Process

After the selection of studies, key data from the eligible studies were extracted using a form created by the authors with predefined items. The main items included first author, year of publication, genus and species of the isolated microorganism, sample type, analytical method for glyphosate biodegradation, intermediate metabolites post-biodegradation, main enzymes related to the glyphosate degradation metabolic pathway, country, and published journal. These data were then tabulated in an Excel spreadsheet, and any additional calculations and tabulations were performed by two researchers.

7. Risk of Bias

Publication bias was assessed using the Joanna Briggs Institute (JBI) critical appraisal checklist for qualitative research [12]. This checklist classifies studies into three levels of risk: high, moderate, and low. High risk is attributed to studies with more than 49% “yes” responses, moderate risk for those with 50–69% “yes” responses, and low risk for studies with 70% or more “yes” responses. Studies with a high risk of publication bias were excluded based on this assessment.

8. Results

A total of 452 articles were systematically found. Of these, 41 were excluded as duplicates, 254 were excluded based on their titles, 52 were excluded based on their abstracts, and 71 studies did not meet the eligibility criteria. This resulted in a total of 34 studies included in this systematic review (Figure 1).
The 34 eligible studies initially involved a systematic analysis of the literature on the prevalence of bacteria with potential glyphosate degradation capacity. Table 1 presents the main genera and species of bacteria, along with key characteristics of each study, such as sample type, analytical method for glyphosate biodegradation, intermediate metabolites post-biodegradation, main enzymes related to the glyphosate degradation metabolic pathway, country, and published journal.
A total of 21 genera and 46 bacterial species related to glyphosate degradation were identified in this systematic review. The most frequent genera were Bacillus (n = 9), Pseudomonas (n = 8), and Ochrobactrum (n = 6), with species including Bacillus sp., B. aryabhattai, B. cereus, B. megaterium, B. subtilis, Pseudomonas sp., P. stutzeri, P. aeruginosa, P. putida, Ochrobactrum sp., O. anthropi, O. rhizosphaerae, O. intermedium, O. hematophilum, and O. Pituitosum (Table 1).
The biodegradation process for this herbicide was evaluated using various methodologies such as High-Performance Liquid Chromatography (HPLC), Electrospray Ionization Mass Spectrometry (ESI-MS), Thin Layer Chromatography (TLC), Gas Chromatography-Mass Spectrometry (GC-MS), Spectrophotometer, UV–Vis Spectrophotometer, Nuclear Magnetic Resonance (NMR), Liquid Chromatography-Isotope Ratio Mass Spectrometry (LC-IRMS), Ultra High-Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS), and Ultra Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry (UPLC-ESI-MS), with HPLC being one of the most commonly used techniques (Table 1).
The main enzymes analyzed were glyphosate oxidoreductase, C-P lyases, glycine oxidoreductase, sarcosine dehydrogenase, sarcosine oxidase, glycine oxidase, C-N lyases, phosphatase, and phosphotriesterase (Table 1). AMPA was the most frequently observed intermediate metabolite, and glyphosate oxidoreductase was the most frequently reported enzyme in these studies.
Furthermore, the key intermediate metabolites resulting from this biodegradation process were identified, including Aminomethylphosphonic Acid (AMPA), Carbon Dioxide (CO2), phosphate, water, sarcosine, glyoxylate, metaphosphoric acid, formaldehyde, inorganic phosphate, glycine, glycolic acid, hydrogen peroxide, methionine, histidine, serine, and cysteine (Table 1). According to the data from this systematic review, the highest number of studies published from 1984 to 2023 was observed in 2021 (Figure 2).
Another approach observed in this study pertains to the main continents and countries that have contributed to this topic by publishing related articles. Figure 3 shows that South and North America lead in the number of publications, with Argentina (16) in first place, followed by the United States (12). The figure also presents the distribution of bacterial genera by continent.
Continuing with the qualitative synthesis regarding scientific journals, out of the 29 journals addressed in this study, 23 had an Impact Factor (IF) as represented in the Journal Citation Reports (JCR) (Figure 4), resulting in an overall average IF of 4.8. However, only six journals were not indexed in the JCR: Biological Diversity and Conservation, Genomics Data, Genetics and Molecular Research, Iraqi Journal of Agricultural Sciences, Microbiology Research Journal International, and Saudi Journal of Biological Sciences.
Regarding the risk of bias according to the JBI checklist, it was observed that the majority of responses in the critical appraisal questionnaire for the studies consisted of > 80% “Yes” responses. This indicates that the eligible studies in this investigation presented a low risk of bias, demonstrating high methodological quality.

9. Discussion

The widespread and unrestricted use of the herbicide glyphosate has threatened the health of non-target plants, animals, humans, and even microorganisms in various ecosystems. Consequently, investigations have been conducted to thoroughly understand the consequences of this herbicide, particularly in carbon mineralization [43].
Most of the isolated microorganisms were obtained from agricultural soils and water bodies contaminated with herbicides. These isolation sites are frequently exposed to intensive glyphosate applications, suggesting that the presence of these herbicides selects and favors microbial populations with degradation capabilities [38]. For example, Bacillus and Pseudomonas species have been isolated from continuously cultivated soils, while Ochrobactrum and Achromobacter have been found in contaminated wastewater and activated sludge [9,13].
This information underscores the importance of investigating the environmental contamination of isolation sites to correlate the presence of these microorganisms with their ability to biodegrade glyphosate in situ. Additionally, identifying contaminated environments provides insights into the applicability of these microorganisms for bioremediation strategies in different environmental contexts [44,45].
Biodegradation is the primary process for eliminating this compound from the environment, and it has been extensively studied in experiments with microorganisms, especially bacteria. Thus, this approach has been investigated in vitro to understand the bacterial capacity to use this herbicide as a source of inorganic phosphorus, as well as nitrogen and carbon [14].
In this context, it is considered that glyphosate biodegradation in water or soil is not only affected by bacterial activity or the composition of herbicide but also by the physical environment in which the compound is found. This physical environment is related to soil characteristics, the rate of glyphosate application, soil management practices, and the processes of herbicide transport to the soil [43].
This review found that glyphosate degradation by bacteria can occur in different environments, both aquatic and terrestrial. Soil and water are the main environments where glyphosate can alter the physical and chemical habitat, resulting in changes in biodiversity. Due to its strong interaction with iron particles, aluminum oxide, and clay, the retention capacity of this herbicide on soil surfaces is high [8,16]. This strong adsorption to specific soil particles means that immediate leaching of glyphosate is considered low and/or insufficient. Some studies demonstrate that due to agricultural practices such as plowing, tilling, and irrigation, as well as rainfall intensity, glyphosate can reach streams and rivers, consequently contaminating not only the water but also the organisms living in those ecosystems. This exposure results in communities of microorganisms in the environment that can develop tolerance and adherence to different types of substrates, as well as acquire mineralization and transformation capacities [8,45]. Therefore, the investigation into understanding the factors and processes involved in glyphosate metabolism has focused on isolating these microorganisms from different environments and consequently optimizing culture conditions through a laboratory enrichment approach. This controlled optimization allows monitoring of pH, temperature, incubation time, inoculum, and herbicide concentration to obtain responses about which bacteria are capable of degrading it [38,42].
Over the years, the literature has shown an increasing number of bacteria capable of degrading glyphosate. Thus, the ability of bacteria to degrade glyphosate is widely distributed across various genera and is not restricted to specific taxonomic groups. The most commonly observed genera include Bacillus, Pseudomonas, Ochrobactrum, Achromobacter, Agrobacterium, and Klebsiella [15,16,42,44]. This review identified the main genera for this purpose as Bacillus, Pseudomonas, and Ochrobactrum.
Thus, glyphosate-degrading bacteria have the ability to decompose this compound into smaller molecules through enzymatic reactions (Figure 5) [46]. There are two main metabolic pathways involved in the degradation of glyphosate by bacteria. The glyphosate oxidation pathway, mediated by the enzyme glyphosate oxidoreductase, results in the formation of AMPA and formaldehyde [14,47]. The second pathway is the C-P lyase pathway, in which the enzyme C-P lyase cleaves the carbon–phosphorus bond, producing sarcosine and inorganic phosphate [8]. These pathways are fundamental for efficient biodegradation and vary among different bacterial genera [7]. Additionally, these enzymes are encoded by specific genes that differ between bacterial genera, reflecting the diversity of biodegradation mechanisms.
The main intermediate metabolites found in the literature include AMPA, sarcosine, glyoxylate, glycine, metaphosphoric acid, and phosphate [7,47]. In this context, glyoxylate, AMPA, and sarcosine can undergo further bacterial degradation. Glyoxylate can be metabolized into glycine and CO2. Additionally, AMPA can be cleaved to produce inorganic phosphate and methylamine. Methylamine can subsequently be degraded into formaldehyde and incorporated into bacterial biomass. Lastly, sarcosine can be cleaved into glycine and formaldehyde and also incorporated into bacterial biomass [8].
The microorganisms listed in Table 1 demonstrate the ability to use glyphosate as a source of carbon, phosphorus, and, in some cases, nitrogen. This process is possible due to the presence of specific enzymes that break down glyphosate into simpler compounds that can be metabolized for energy production [14,48]. For example, genera such as Bacillus, Pseudomonas, and Ochrobactrum are known to metabolize glyphosate and its intermediates, such as AMPA (aminomethylphosphonic acid) and sarcosine, into usable substrates [10,39].
During glyphosate degradation, the accumulation of intermediate metabolites, primarily AMPA and sarcosine, [13,14]. Although some microorganisms can metabolize these additional compounds, the persistence of AMPA in the environment is concerning due to its toxicity, which is similar to that of glyphosate [2,49]. Sarcosine can also accumulate in environments where degradation is not entirely efficient [42].
Intermediate metabolites from glyphosate degradation, especially AMPA, pose significant environmental risks. Studies indicate that AMPA can cause adverse effects in aquatic and terrestrial organisms, including endocrine dysfunctions and growth problems [50,51]. Therefore, the presence of these intermediates in the environment requires ongoing attention and mitigation strategies to prevent long-term environmental impacts [2].
The uniformity of the enzymes and metabolites listed in Table 1 across different bacterial types suggests that there are indeed conserved metabolic pathways for glyphosate degradation among various bacterial species. The two main biodegradation pathways, the glyphosate oxidoreductase pathway, which produces AMPA (aminomethylphosphonic acid), and the C-P lyase pathway, which generates sarcosine and inorganic phosphate, have been observed in genera such as Bacillus, Pseudomonas, Ochrobactrum, and Achromobacter [8,14]. This consistency suggests that the evolution of these metabolic pathways may have occurred in parallel or through horizontal gene transfer (HGT), facilitating the spread of glyphosate-degrading genes among different bacterial species [38,42].
Despite the similarity in metabolic pathways, factors such as enzyme efficiency, optimal environmental conditions, and genetic regulation can vary among species, influencing the overall effectiveness of degradation. For instance, Bacillus cereus may exhibit high glyphosate degradation efficiency under neutral pH conditions [40], while Pseudomonas putida may have greater tolerance to environments with additional contaminants [4].
This uniformity also suggests that applying combined bioremediation strategies using consortia of different species can be advantageous, leveraging the robustness of conserved pathways and the complementary adaptive capabilities of individual species. Additional studies should explore the genetic regulation of these pathways in different species and investigate potential adaptive mutations that could optimize degradation under specific contaminated environmental conditions [38,41].
The adaptive capacity of bacterial glyphosate biodegradation results from selective pressure in contaminated environments, leading to the evolution of specialized metabolic pathways. Furthermore, horizontal gene transfer (HGT) plays a crucial role in disseminating glyphosate-degrading genes. Genes encoding these degrading enzymes can be transferred between bacterial species via plasmids, transposons, and integrative conjugative elements [8,42]. This transfer facilitates the rapid adaptation of microbial communities to glyphosate-contaminated environments, increasing the likelihood of finding degradative microorganisms in diverse ecological niches.
Understanding the ecology and evolutionary dynamics of degradative microorganisms is essential for optimizing bioremediation strategies. For example, identifying microbial communities with a high potential for horizontal gene transfer may enable the creation of synthetic microbial consortia that are more effective in field-based glyphosate degradation [39]. Additionally, studying the evolution of these genes can provide insights into the resilience and resistance of microbial populations in contaminated sites.
Besides primary glyphosate-degrading microorganisms, other environmental microbes can contribute to the mineralization of intermediate metabolites. Pseudomonas, Achromobacter, and Bacillus species have demonstrated the ability to degrade AMPA into less toxic compounds, such as inorganic phosphate and methylamine [38,52]. This microbial interaction is crucial for the complete biodegradation process and for the environmental recovery of contaminated areas [8,42].
The analytical methodology for the herbicide glyphosate and its metabolites has seen numerous studies utilizing LC-MS as a detector or with derivatization processes and UV–Visible or fluorescence detection, in addition to GC-MS and spectroscopic and electrochemical methods. These methods have been used for simpler, faster, and even more sensitive analyses for the quantification of this herbicide in environmental, biological, and food samples [53].
Studies show different effects of glyphosate depending on the organism. For example, microorganisms exhibit minimal acute toxicity, unlike terrestrial and aquatic organisms. In these organisms, depending on the concentration of glyphosate, toxic effects can be observed, such as endocrine dysfunctions, reproductive problems, growth issues, tumors, and liver, heart, and blood problems [2,50,51].
According to this investigation, South and North America lead in the number of publications on glyphosate biodegradation. This is likely due to the extensive use of this herbicide in local agriculture. Argentina and the United States, in particular, are large agricultural producers that heavily depend on glyphosate for weed control [54,55].
The high application of glyphosate in these countries creates a critical need to understand and mitigate its environmental impacts, driving research into the biodegradation of this compound. Consequently, both countries have invested significantly in scientific and biotechnological research to develop and optimize biodegradation processes, reflected in the high number of academic publications on the topic.
As a result, glyphosate bioremediation technologies have been developed to remove the toxic effects, particularly of its metabolite AMPA. In most cases, bacteria are used as a degradation strategy for this herbicide and its metabolites into less harmful compounds, with pure strains and bacterial consortia identified to evaluate bioremediation efficiency, primarily with isolates from water and soil sources contaminated by this pesticide [54]. This is a promising alternative for eliminating this pollutant, making it less harmful to the environment. Consequently, investigations have continuously strived to find more sustainable and economically viable solutions, contributing to a promising environmentally sustainable and responsible future.
Figure 2 reveals a significant spike in the number of studies identifying glyphosate-degrading microorganisms in 2021. This increase can be attributed to several converging factors. Firstly, there was a rise in environmental and public health concerns related to the extensive use of glyphosate following the classification of this herbicide as “probably carcinogenic” by the International Agency for Research on Cancer (IARC) in 2015 [3]. This classification spurred scientific interest in alternative methods to mitigate the environmental impacts of glyphosate, such as bioremediation [55].
Furthermore, changes in public policies and environmental regulations in countries with high agricultural glyphosate usage, such as Argentina and the United States, encouraged funding for research focused on the biodegradation of this compound [56,57]. The increasing visibility of this topic at international conferences and its publication in high-impact journals also contributed to this surge [58,59].
The sharp decline after 2021 may be explained by a temporary saturation of research in this specific area, as the published studies had already covered the main microorganisms and metabolic pathways known at the time. Additionally, funding constraints and shifts in research priorities during the COVID-19 pandemic may have affected the continuity of new studies [59]. Another possible factor is the technical challenge of applying these discoveries on a practical scale. Implementing bioremediation strategies in the field faces barriers related to environmental variability and high costs, which may have reduced the momentum for further investigations focused solely on identifying degraders [8,60].
This investigation also addressed the Impact Factor (IF) according to the JCR. This criterion is important as it reveals the number of works published in high-IF journals, highlighting the dissemination of quality research and increasing the visibility and credibility of the studies conducted [61]. Additionally, journals with higher impact factors, such as the Journal of Hazardous Materials (13.6) and The ISME Journal (12.3), are recognized for their scientific rigor and scope, facilitating the inclusion of new knowledge in scientific and industrial practice. Therefore, by selecting high-impact journals for publications, these researchers contribute more significantly to the advancement of science and the implementation of innovative biotechnological solutions for glyphosate bioremediation, contributing to this highly relevant and essential topic for quality of life and the environment.
By consolidating this information, we provide a solid foundation for future research and the development of biotechnological strategies for bioremediation. Moreover, this review emphasizes the importance of continuous investigations to optimize environmental conditions and make large-scale applications feasible. Thus, this investigation strengthens existing knowledge and serves as a valuable resource for scientists, policymakers, and environmental professionals, promoting sustainable practices and more informed policies for herbicide management.

10. Conclusions

This review synthesized the main microorganisms capable of degrading glyphosate, addressing their metabolic pathways, the enzymes involved, and the intermediates formed. The results provide a solid foundation for applying these microorganisms in environmental bioremediation strategies. However, transitioning these laboratory findings to the field requires a deep understanding of real environmental conditions. These conditions refer to the variable and complex factors found in nature, such as temperature, pH, soil moisture, the presence of additional contaminants, native microbial composition, and interactions with other species, which differ from the controlled conditions of laboratory experiments.
For glyphosate-degrading microorganisms to be effective in natural environments, it is necessary to address challenges such as adaptation to environmental variations, competition with native microbiota, and the presence of multiple contaminants. Microorganisms like Bacillus, Pseudomonas, and Ochrobactrum show potential for glyphosate degradation in the laboratory, but their effectiveness in the field may be limited if they are not adapted to these variabilities. Strategies such as using microbial consortia, which combine different species to enhance degradation efficiency, can help overcome competition with native microorganisms. Additionally, immobilizing microorganisms on biocompatible supports and employing bioaugmentation techniques can improve their survival and persistence in the environment.
Thus, this review emphasizes the importance of conducting controlled field studies that consider environmental variability and test the effectiveness of microorganisms in glyphosate-contaminated sites. Therefore, this study not only expands scientific understanding but also provides practical guidelines for efficiently applying bioremediation in glyphosate-impacted areas. Future investigations should focus on metagenomic and functional studies to identify new degradative genes and better understand their interactions in complex ecosystems.

Author Contributions

All authors contributed to the conception and design of the study. The preparation of the material and data collection were carried out by K.S.S., M.R.F.d.S., M.A.C., H.T.S.L., and G.d.L.T. Data analysis was carried out by K.C.d.S.F., K.C.C.S., R.M.N.F., L.C.A.d.A., and F.M. The critical review of the manuscript was carried out by R.B., S.T., R.S., M.D.V.S., I.P.S.S., A.V.d.B., and M.B.M.d.O. All authors have read and agreed to the published version of the manuscript.

Funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by Coordination for the Improvement of Higher Education Personnel (CAPES/Brazil—Proc. no 88887.500819/2020-00). Financial support provided by FACEPE—APQ 1120-3.07/22 (Foundation for the Support of Science and Technology of the State of Pernambuco).

Informed Consent Statement

All study participants gave their informed consent to participate in this research. All study authors and participants gave their consent for the publication of the results of this research.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Agronomy 15 01247 g001
Figure 1. Flowchart with quantitative and qualitative data of excluded and included articles.
Figure 1. Flowchart with quantitative and qualitative data of excluded and included articles.
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Figure 2. Number of studies published on glyphosate degradation involving bacteria.
Figure 2. Number of studies published on glyphosate degradation involving bacteria.
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Figure 3. Distribution of genera and published studies by continent and country.
Figure 3. Distribution of genera and published studies by continent and country.
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Figure 4. Impact factor of scientific journals publishing bacteria-mediated degradation of glyphosate.
Figure 4. Impact factor of scientific journals publishing bacteria-mediated degradation of glyphosate.
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Figure 5. Glyphosate handling routes.
Figure 5. Glyphosate handling routes.
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Table 1. Main bacteria described in the literature with the potential for glyphosate degradation.
Table 1. Main bacteria described in the literature with the potential for glyphosate degradation.
GenusSpeciesSourceBiodegradation AnalysisMetabolitesEnzymesJournalReference
AchromobacterAchromobacter sp.SoilSpectrophotometry and NMR *AMPA *Glyphosate OxidoreductaseScience of the Total Environment[13]
Activated SludgeHPLC *C-P LyasesJournal of Industrial Microbiology[14]
SoilInorganic PhosphateApplied and Environmental Microbiology[15]
AcidovoraxAcidovorax sp.WaterHPLC *AMPA *, Sarcosine, Formaldehyde e GlycineC-P Lyases, Glycine OxidoreductaseJournal of Hazardous Materials[9]
AgrobacteriumAgrobacterium tumefaciensSoilSpectrophotometry and NMR *AMPA *Glyphosate OxidoreductaseScience of the Total Environment[13]
WaterHPLC *AMPA *, Sarcosine, Formaldehyde e GlycineC-P Lyases, Glycine OxidoreductaseJournal of Hazardous Materials[9]
Agrobacterium radiobacterActivated SludgeAMPA *C-P LyasesJournal of Industrial Microbiology[14]
AlcaligenesAlcaligenes sp.Water e SoilHPLC *AMPAC-P LyasesCurrent Microbiology[16]
Laboratory CultureTLC *AMPA *, Sarcosine, GlycineArchives of Microbiology[17]
ArthrobacterArthrobacter sp.SoilTLC *Glycine, Sarcosine, Formaldehyde, Methionine, Histidine, Serine, CysteineC-P Lyases, Sarcosine Dehydrogenase Sarcosine and OxidaseEuropean Journal of Biochemistry[18]
BacillusBacillus sp.SoilSpectrophotometryAMPA *, SarcosineC-P LyasesGroundwater for Sustainable Development[19]
Bacillus aryabhattaiSpectrophotometry UV–VisAMPA *, SarcosineGlyphosate Oxidoreductase, Sarcosine and OxidaseSaudi Journal of Biological Sciences[20]
Spectrophotometry and NMR *AMPA *Glyphosate OxidoreductaseScience of the Total Environment[13]
Bacillus cereusGC-MS *AMPA *C-P Lyases Glyphosate OxidoreductaseMicrobiology Research Journal International[21]
HPLC *AMPA *, Sarcosine, Formaldehyde, Glyoxylate e GlycineGlyphosate Oxidoreductase, C-P LyasesJournal of General and Applied Microbiology[22]
Inorganic Phosphate, PolyphosphateC-P LyasesThe ISME Journal[23]
Bacillus megateriumAMPA *, Sarcosine, Formaldehyde, Glyoxylate e GlycineGlyphosate Oxidoreductase, C-P LyasesIraqi Journal of Agricultural Sciences[24]
Bacillus subtilisESI-MS *, HPLC *AMPA *, Sarcosine, Glyoxylate, Metaphosphoric Acid, PhosphateC-P Lyase, Glyphosate OxidoreductaseJournal of Environmental Chemical Engineering[25]
Spectrophotometry UV–Vis--Genetics and Molecular Research[26]
BradyrhizobiumBradyrhizobium sp.SoilUPLC-ESI-MS *AMPA *Oxidase of Glycine, C-P LyasesCurrent Microbiology[27]
Bradyrhizobium japonicum
Bradyrhizobium diazoefficiens
Bradyrhizobium ottawaense
Bradyrhizobium lablabi
Bradyrhizobium erythrophlei
Bradyrhizobium jicamae
Bradyrhizobium elkanii
Bradyrhizobium canariense
Bradyrhizobium lupini
Bradyrhizobium icense
ChryseobacteriumChryseobacterium sp.Activated SludgeHPLC *,
LC-MS *		AMPA *, Glycolic Acid, Hydrogen PeroxideOxidase of GlycineJournal of Agricultural and Food Chemistry[28]
SoilUPLC-MS *AMPA *, Glyoxylate, Sarcosine, GlycineC-N LyasesJournal of Hazardous Materials[29]
ComamonasComamonas odontotermitisSoilHPLC *AMPA *, Sarcosine, GlycineGlyphosate Oxidoreductase C-P LyasesPedosphere[30]
EnsiferEnsifer sp.SoilHPLC *AMPA *, CO2 *, Phosphate and WaterPhosphatase, PhosphotriesteraseInternational Journal of Applied and Natural Sciences[31]
EnterobacterEnterobacter sp.SoilHPLC *AMPA *C-P LyasesGenomics Data[32]
GeobacillusGeobacillus caldoxylosilyticusWaterHPLC *, NMR *AMPA *, GlyoxylateGlyphosate OxidoreductaseApplied and Environmental Microbiology[33]
KlebsiellaKlebsiella variicolaSoilSpectrophotometryAMPA *-Biological Diversity and Conservation[34]
Spectrophotometry and NMR *Glyphosate OxidoreductaseScience of the Total Environment[35]
WaterSpectrophotometry UV-VisC-P LyasesSaudi Journal of Biological Sciences[34]
Klebsiella pneumoniaeSoilSpectrophotometry-Biological Diversity and Conservation[34]
Spectrophotometry and NMR *Glyphosate OxidoreductaseScience of the Total Environment[13]
LysinibacillusLysinibacillus sphaericusSoilUHPLC-MS *AMPA *, SarcosineSarcosine OxidaseAgriculture[36]
NovosphingobiumNovosphingobium sp.WaterHPLC *AMPA *, Sarcosine, Formaldehyde e GlycineC-P Lyases, Glycine OxidoreductaseJournal of Hazardous Materials[9]
OchrobactrumOchrobactrum sp.SoilSpectrophotometry and NMR *AMPA *Glyphosate OxidoreductaseScience of the Total Environment[13]
HPLC *Glyphosate OxidoreductaseJournal of Environmental Science and Health[37]
Ochrobactrum anthropiNMR *, LC-IRMS *--Environmental Science & Technology[38]
HPLC *Inorganic PhosphateC-P LyasesApplied and Environmental Microbiology[15]
Ochrobactrum rhizosphaeraeNMR *,
LC-IRMS *		--Environmental Science & Technology[38]
Ochrobactrum intermedium
TLC, HPLCSarcosine and GlycineC-P LyasesPest Management Science[30]
Ochrobactrum hematophilumNMR *, LC-IRMS *--Environmental Science & Technology[38]
Ochrobactrum pituitosum
WaterHPLC *AMPA *, Sarcosine, Formaldehyde and GlycineC-P Lyases, Glycine OxidoreductaseJournal of Hazardous Materials[9]
PantoeaPantoea stewartiiWaterSpectrophotometry UV-VisAMPA *C-P LyaseSaudi Journal of Biological Sciences[35]
ProvidenciaProvidencia rettgeriSoilHPLC *AMPA *Glyphosate Oxidoreductase, C-P LyaseJournal of Bioscience and Bioengineering[39]
PseudomonasPseudomonas sp.SoilSpectrophotometryAMPA *, SarcosineC-P LyasesGroundwater for Sustainable Development[19]
WaterSpectrophotometry UV–VisAMPA *C-P LyasesSaudi Journal of Biological Sciences[35]
SoilTLC *SarcosineC-P LyasesFEMS Microbiology Letters[40]
Sarcosine DesidrogenaseThe Journal of Biological Chemistry[41]
Water and SoilHPLC *AMPA *C-P LyasesCurrent Microbiology[16]
Soil and SludgeSpectrophotometryApplied Microbiology and Biotechnology[42]
Pseudomonas stutzeriWater and SoilHPLC *Current Microbiology[16]
Pseudomonas aeruginosaSoilGC-MS *C-P Lyases Glyphosate OxidoreductaseMicrobiology Research Journal International[21]
Pseudomonas putidaTLC *, HPLC *Glyphosate OxidoreductaseMicroorganisms[5]
RhizobiumRhizobium sp.SoilHPLC *AMPA *, CO2 *, Phosphate and WaterPhosphatase, PhosphotriesteraseInternational Journal of Applied and Natural Sciences[31]
Rhizobium leguminosarumESI-MS *, HPLC *AMPA *, Sarcosine, Glyoxylate, Metaphosphoric Acid, PhosphateC-P Lyases, Glyphosate OxidoreductaseJournal of Environmental Chemical Engineering[25]
SinorhizobiumSinorhizobium saheliSoilHPLC *AMPA *, CO2 *, Phosphate and WaterPhosphatase, PhosphotriesteraseInternational Journal of Applied and Natural Sciences[31]
* HPLC (High-Performance Liquid Chromatography), ESI-MS (Electrospray Ionization Mass Spectrometry), TLC (Thin Layer Chromatography), GC-MS (Gas Chromatography-Mass Spectrometry), Spectrophotometer, UV–Vis Spectrophotometer, NMR (Nuclear Magnetic Resonance), LC-IRMS (Liquid Chromatography-Isotope Ratio Mass Spectrometry), UHPLC-MS (Ultra High-Performance Liquid Chromatography-Mass Spectrometry), UPLC-ESI-MS (Ultra Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry), AMPA (Aminomethylphosphonic Acid), CO2 (Carbon Dioxide).
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Souza, K.S.; da Silva, M.R.F.; Candido, M.A.; Lins, H.T.S.; de Lima Torres, G.; da Silva Felix, K.C.; Silva, K.C.C.; Filho, R.M.N.; Bhadouria, R.; Tripathi, S.; et al. Biodegradation Potential of Glyphosate by Bacteria: A Systematic Review on Metabolic Mechanisms and Application Strategies. Agronomy 2025, 15, 1247. https://doi.org/10.3390/agronomy15051247

AMA Style

Souza KS, da Silva MRF, Candido MA, Lins HTS, de Lima Torres G, da Silva Felix KC, Silva KCC, Filho RMN, Bhadouria R, Tripathi S, et al. Biodegradation Potential of Glyphosate by Bacteria: A Systematic Review on Metabolic Mechanisms and Application Strategies. Agronomy. 2025; 15(5):1247. https://doi.org/10.3390/agronomy15051247

Chicago/Turabian Style

Souza, Karolayne Silva, Milena Roberta Freire da Silva, Manoella Almeida Candido, Hévellin Talita Sousa Lins, Gabriela de Lima Torres, Kátia Cilene da Silva Felix, Kaline Catiely Campos Silva, Ricardo Marques Nogueira Filho, Rahul Bhadouria, Sachchidanand Tripathi, and et al. 2025. "Biodegradation Potential of Glyphosate by Bacteria: A Systematic Review on Metabolic Mechanisms and Application Strategies" Agronomy 15, no. 5: 1247. https://doi.org/10.3390/agronomy15051247

APA Style

Souza, K. S., da Silva, M. R. F., Candido, M. A., Lins, H. T. S., de Lima Torres, G., da Silva Felix, K. C., Silva, K. C. C., Filho, R. M. N., Bhadouria, R., Tripathi, S., Singh, R., Santos, M. D. V., Silva, I. P. S., de Barros, A. V., de Araújo, L. C. A., Motteran, F., & de Oliveira, M. B. M. (2025). Biodegradation Potential of Glyphosate by Bacteria: A Systematic Review on Metabolic Mechanisms and Application Strategies. Agronomy, 15(5), 1247. https://doi.org/10.3390/agronomy15051247

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