2.1 Annual distribution of type of document and citations
A total of 105 documents were included in our database where 91 documents (87%) corresponded to research articles, and 14 documents (13%) were reviews. The oldest document in the database was published in 1990 (Schlömann et al. 1990). The most impactful study before the turn of the 21st century was Key et al. (1998). In Key et al.’s pioneering study, the authors explored the potential of fluorinated sulfonate biodegradation by Pseudomonas sp. D2. They found that only polyfluorinated compounds containing hydrogen, such as 2,2,2-trifluoroethane sulfonate (TES) and 1H,1H,2H,2H-perfluorooctane sulfonate (H-PFOS), were completely or partially defluorinated, respectively. Alternatively, perfluorinated compounds, such as trifluoromethane sulfonate (TFMS) and perfluorooctane sulfonate (PFOS), were not biodegraded (Key et al. 1998). Figure 2 depicts the numbers of publications and citations per year of microbial defluorination studies. Figure 2 shows a general increasing number of publications per year in this young and steadily growing field. The highest number of documents published in one year is 11 during 2022 (Fig. 2). The peaks in citations in 1998 and 2013 come from Key et al. 1998 (179 citations) and Jinxia et al. 2013 (317 citations), the first and third most cited publications in the database.(Key et al. 1998, Jinxia and Sandra Mejia 2013).
In order to unlock other scientific relationships in the development of the microbial defluorination field, we performed a sideways analysis of references cited by the search query-established database via Biblioshiny (Aria and Cuccurullo 2017). A total of 5093 references were cited in our database (105 publications). The earliest document is from 1930 and is a foundational reference on the relationships between enzymes and substrates (Haldane 1930) but does not directly focus on defluorination. The second earliest cited article (from 1944) established monofluoroacetic acid as the toxic component of the gifblaar (Dichapetalum cymosum) “poison leaf” plant (Marais 1944). The most cited article (16 citations) prior to 1990, which is the earliest publication in our database, presents an experimental analysis of bacteria capable of using fluoroacetate as a sole carbon source and releasing fluoride ions via the action of an unnamed enzyme (Goldman 1965). According to our search, Goldman (1965) is the earliest use of the word “defluorination” in a title from the surveyed literature. The next four topmost referenced citations prior to 1990 focus on defluorination of fluorinated aromatic compounds (Lowry et al. 1951, Schennen et al. 1985, Oltmanns et al. 1989, Renganathan 1989) and should be considered forerunners to the experimental articles presented in the database. When we perform the same analysis after 1990, the top five most referenced articles focus on complex fluorinated organics in the environment and their biotransformation (Key et al. 1997, Dinglasan et al. 2004, O'Hagan 2008, Murphy 2010, Huang and Jaffé 2019). These articles elaborate on the structure-dependent relationship between fluorinated compounds and how microbes cleave C − F bonds (Key et al. 1997, Dinglasan et al. 2004, O'Hagan 2008, Murphy 2010, Huang and Jaffé 2019). Analyzing common shared references identifies pioneering articles which either furthered or established foundational knowledge for the microbial defluorination field.
To establish the scope of the most recent updates on microbial defluorination literature, we analyzed the five most cited papers in our database from 2018 to 2023. We consider these papers to be representative of recent research interest and important for determining the current state of the science. The most cited paper from 2018 to 2023 was Shaw et al. (2019) with 92 citations. Shaw et al. (2019) employed a pure culture of Gordonia sp. strain NB4-1Y to degrade 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), two PFAS compounds which are typical constituents of aqueous film forming foams (AFFFs). The study documented 6:2 FTAB and 6:2 FTSA biotransformation into 16 identified metabolites, including 6:2 fluorotelomer acid (6:2 FTCA), 6:2 fluorotelomer unsaturated acid (6:2 FTUA), and 5:3 fluorotelomer acid (5:3 FTCA).49 Biotransformation decreased the initial concentrations of 6:2 FTSA and 6:2 FTAB by 99.9% and 70.4%, respectively, during 168 hours of incubation (Shaw et al. 2019).
The second most cited publication is Gao et al. (2018) with 53 citations. Gao et al. (2018) found that Pycnosporus sanguines was more effective than Phanerochaete chrysosporium at biotransformation of the fluorinated antibiotics ciprofloxacin and norfloxacin and the non-fluorinated antibiotic sulfamethoxazole. Gao et al. (2018) elucidated antibiotic biotransformation pathways, including defluorination as an explanation for a defluorinated biotransformation product referred to as m/z 286 (Gao et al. 2018).
The third most cited publication is Yu et al. (2020) with 43 citations. Yu et al. (2020) used a Dehalococcoides mccartyi-containing enrichment culture that reductively defluorinated (E)-perfluoro (4-methylpent-2-enoic acid) (PFMeUPA) and 4,5,5,5-tetrafluoro-4-(trifluoromethyl)-2-pentenoic acid (FTMeUPA). PFMeUPA and FTMeUPA achieved > 90% transformation to products from microbial hydrogenation (Yu et al. 2020). However, FTMeUPA was biotransformed faster (70 d) than PFMeUA (130 d) with defluorination extents of 4–5% and 14% for FTMeUPA and PFMeUPA, respectfully. Dehalobacter, but not Dehalococcoides mccartyi or Geobacter sp., or other microorganisms present in the mixed culture were postulated to be responsible for the defluorination of these two PFAS molecules (Yu et al. 2020).
The fourth most cited publication was Li et al. (2018) with 33 citations. Li et al. (2018) analyzed the anaerobic biodegradation of 8:2 fluorotelomer alcohol (8:2 FTOH) in anaerobic activated sludge and found it was biodegraded into various poly- and perfluorinated metabolites with documented fluoride ion release. The most abundant metabolites were 8 − 2 fluorotelomer unsaturated acid (8:2 FTUA) and perfluorooctanoate (PFOA). A biodegradation pathway beyond those metabolites was also expounded (Li et al. 2018).
The fifth most cited paper in our database from 2018 to 2023 was Cerro-Gálvez et al. (2020) with 25 citations. The authors explored the effects of perfluorooctanesulfonate (PFOS) and PFOA on Antarctic marine microbial communities. The study found that concentrations of PFOS decreased by more than 50% after 48 hours with an increase in sulfur metabolism-related biomarkers (Cerro-Gálvez et al. 2020). No significant differences were found between the initial and final PFOA concentration. Furthermore, Gammaproteobacteria and Roseobacter increased in relative abundance after 24 hours, while Flavobacteriia increased after 6 days of incubations. The authors assert that these factors plus an increase in extracellular enzyme activity and absolute number of transcripts in the PFAS exposed treatments signify selection of PFOS and PFOA tolerant microbial consortia. These results link PFOS biotransformation directly to the ocean’s sulfur biogeochemistry (Cerro-Gálvez et al. 2020). While the five featured papers from 2018 to 2023 do not fully capture the diversity of microbial defluorination science, they do provide a valuable snapshot of the field. From these studies, we see PFAS biotransformation research is focused on identifying defluorinating bacteria and pathways involved in defluorination.
2.2 Analysis of keyword usage, evolution, and co-occurrence linkage in microbial fluorinated compound biodegradation literature
Figure 3 depicts the co-occurrence trends of all keywords seen in our database. There were 1988 total keywords in the database and 68 met the minimum 6 occurrences threshold. Figure 3 uses the size of the colored circles to indicate occurrence frequency, the lines between circles to indicate keyword relation, and keyword coloring to depict thematic relation (Fig. 3A), average publication year (Fig. 3B), and number of citations (Fig. 3C).
In Fig. 3A, each color corresponds to a cluster created based on the grade of similarity among keywords. The largest circles, and therefore the most frequent keywords, are bacteria, biodegradation, bioremediation, defluorination, metabolic pathways, and dehalogenation. These frequently found keywords were, in most cases, directly included in the search query. The high frequency of keywords present in the search query in the generated network is an unavoidable search result bias inherent when finding scientific literature by keyword. Further keyword analysis in terms of subject matter, temporal distribution, and citation numbers allows for a greater depth of understanding of the field.
Thematic division of keywords by color in Fig. 3A affords a general understanding of the types of research being conducted in microbial defluorination science. From the colors in Fig. 3A, it appears that microbial processes (red), biological degradation of contaminants (yellow), PFAS biotransformation (blue), methods of assessing microbial biotransformation processes (green), and wastewater treatment (purple) are the general foci of microbial defluorination research to date. Overall keywords pertaining to microbial processes (red) dominate the network visualization. The categorization by average publication year (Fig. 3B) and number of citations (Fig. 3C) allows for a greater understanding of the evolution of keyword importance over time.
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Figure 3: Microbial defluorination keyword network visualization. A) Thematic keyword visualization. Red keywords pertain to microbial processes. Yellow keywords pertain to biological degradation of contaminants. Blue keywords pertain to PFAS transformation. Green keywords pertain to assessing microbial biotransformation processes. Purple keywords pertain to wastewater treatment. B) Average publication year keyword visualization. Darker colors (purple) represent older keywords and the brighter colors (yellow) are the most recent keywords. C) Average citation number keyword visualization. Darker colors (purple) represent less cited keywords and the brighter colors (yellow) are the more cited keywords. |
Figure 3B defines keywords by their average publication year. The timescale is auto generated by Vosviewer as an average year of publication for each keyword. Newer keywords pertain to identifying and better understanding bacterial communities capable of PFAS biotransformation (i.e., defluorination, PFOA, PFOS, fluorocarbon, biotechnology, microbial community). Older keywords pertain to microbial defluorination’s relationship with microbial dechlorination and establishing methods by which to assess microbial defluorination (i.e., dehalogenation, dechlorination, high performance liquid chromatography (HPLC), gas chromatography, soil microbiology). Therefore, as this field progressed, advancement occurred from verifying analytical chemistry methods for fluorinated compounds to identifying defluorinating bacteria in microbial communities and biochemical pathways for biodegradation. Originally, heavily fluorinated compounds were thought to persist by resisting biodegradation for millennia. Now, knowledge has been obtained on specific microbes capable of defluorination, the enzymes involved in fluorinated compound transformation, and the structure dependent relationship of biotransformation in fluorinated compounds. Biodegradation pathway mapping allows for monitoring and management of relevant biochemical processes needed to create pollutant degradation biotechnologies. Mapping these pathways allows for more conclusive mass balances and enables determination of intermediate compounds, rate limiting steps, and verification of the implications of stalled biotransformation. A seminal example is the reductive dechlorination pathway of tetrachloroethene and trichloroethene (TCE) to ethene (Robles et al. 2021, Mohana Rangan et al. 2023). If appropriate conditions are not maintained or provided during reductive dechlorination, the toxic intermediates, dichloroethene and vinyl chloride, can accumulate instead of the innocuous and non-chlorinated end product, ethene. Therefore, mapping biotransformation pathways of fluorinated compounds is a critical step towards being able to manage contaminated sites and waste streams.
In Fig. 3C we overlayed the network map with the average number of citations per keyword. Yellow keywords such as PFOA, PFOS, reductive dehalogenation, organofluorine compounds, microbial activity, and environmental pollutants have the highest number of citations. Interestingly, these keywords are not the most common, in that they do not have the largest circles yet have the most citations. These keywords are related to microbial biotransformation of PFAS molecules. Though keywords such as bacteria, biodegradation, and defluorination have larger circles indicating their greater commonness, they have a lower average number of citations. PFOS, PFOA, microbial activity and organofluorine compounds also appear to be currently popular keywords (yellow color in Fig. 3B). Therefore, as the field has gained momentum in terms of the number of publications in recent years, the aforementioned keywords, though less common, were associated with papers with a high number of citations. While the database contains microbial defluorination studies on fungicides, antibacterial compounds, and pharmaceuticals, it is clear from the five most cited papers in the last from 2018 to 2023 and the recently highly cited keywords that PFAS biotransformation is currently dominating the microbial defluorination field.
2.3 Countries collaboration and performance
Figure 4 shows the collaboration network of countries that contribute to research on microbial fluorinated compound biodegradation with a total of 33 countries contributing. To examine subject matter trends by each country, we sorted publications by country of origin and analyzed publications in terms of the contaminants being studied, number of publications, and collaboration with research groups from other countries. Publications with authors from multiple countries and co-citation were considered indications of collaboration.
The United States (41 publications), China (27 publications), and Germany (12 publications) are the most prolific contributing countries. The United States, in addition to focusing upon PFAS biodegradation (Key et al. 1998, Dimitrov et al. 2004, Liou et al. 2010, Kim et al. 2012, Lewis et al. 2016, Li et al. 2018, Xie et al. 2020), is clearly focused on assessing the biodegradation of various fluorinated antibiotics and fungicides.(Key et al. 1998, Seeger et al. 2003, Shah and Thakur 2003, Dimitrov et al. 2004, Garbi et al. 2006, Liou et al. 2010, Kim et al. 2011, Camboim et al. 2012, Kim et al. 2012, Amorim et al. 2013, Wang et al. 2014, Carvalho et al. 2016, Lewis et al. 2016, Alexandrino et al. 2017, Zhang et al. 2017, Alexandrino et al. 2018, Li et al. 2018, Duarte et al. 2019, Alexandrino et al. 2020, Fernandes et al. 2020, Xie et al. 2020). This reflects the diversity of environmental concern that various fluorinated chemicals have elicited in the United States. China, in addition to PFAS biodegradation studies, is interested in the biodegradation of fluoroanilines and fluorobenzenes (Zhang et al. 2006, Chaojie et al. 2007, Shen et al. 2014, Zhang et al. 2014, Zhang et al. 2015, Zhang et al. 2015, Li et al. 2016, Wang et al. 2016, Alexandrino et al. 2017, Feng et al. 2017, Gao et al. 2018, Li et al. 2018, Xu et al. 2019, Zhao et al. 2019, Xiang et al. 2020, Xie et al. 2020, Zhao et al. 2020, Fan et al. 2021, Guo et al. 2021). Germany, unlike China and the United States, does not have PFAS-focused microbial biotransformation studies in the database. Germany’s publications focus is on fluorinated benzoates, chlorofluorocarbons, and quinolones, and on fluorosubstituted aromatics ( Schlömann et al. 1990, Krone and Thauer 1992, Karl et al. 2006, Kiel and Engesser 2015).
The generation of microbial fluorinated compound biodegradation knowledge involves efforts with and without collaboration between countries, as seen in Fig. 4. One cluster with 28 countries was identified using VOSviewer. The cluster included connected collaboration and co-citations with all countries, except Italy (1 publication), New Zealand (1 publication), Ireland (3 publications), Iran (1 publication), and Finland (1 publication) (Fig. 4). Overall, there is significant international collaboration among nations producing microbial defluorination science with only 7% of publications coming from non-coupled countries. However, with only 33 countries contributing to knowledge generation, participation of more countries would enhance the rate of microbial defluorination science maturation.
2.4 Analysis of academic department and institution contribution to microbial fluorinated compound biodegradation
Table 1 depicts the top ten institutions contributing to the field of microbial defluorination science ranked first by the number of articles and citations. Table 1 was generated by sorting the database by institution, verifying the number of produced articles, and summing the number of citations associated with each article. We used the interactive data visualization software Power BI for this data analysis and presentation. Ranking institutions by number of articles or by number of citations produces differing outcomes. Therefore, Table 1 is presented to identify highly productive institutions/departments contributing to the microbial defluorination field rather than to make assertions upon which department/institution contributed the most.
The ranking systems in Table 1 reiterate the dominance of China, Portugal, and the United States in microbial fluorinated compound biodegradation research. Additionally, three departments from the University of Porto, Portugal, and two departments from Zhejiang Gongshang University, China, appear separately with different high impact metrics. When collaboration mapping is carried out based on institution, only 8 out of 161 contributing institutions engage in collaboration.
Table 1
Top ten departments ranked by number of articles published.
Department/Institution | Number of articles | Number of citations |
School of Environmental Science and Engineering, Zhejiang Gongshang University, China | 8 | 90 |
Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada | 7 | 399 |
Faculty of Sciences, University of Porto, Porto, Portugal | 6 | 192 |
Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang | 6 | 78 |
Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal | 4 | 176 |
Department of Microbiology, Cornell University, Ithaca, NY, USA. | 4 | 143 |
College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China | 4 | 37 |
Biotechnology Institute, University of Minnesota, United States | 3 | 47 |
College of Environment & Resource Sciences, Zhejiang University, Hangzhou, China | 3 | 8 |
College of Chemical & Material Engineering, Suzhou University, Quzhou, China | 3 | 8 |
Microbial Engineering/University of Minnesota/St. Paul/MN//United States | 2 | 11 |
2.5 Distribution of microbial fluorinated compound biodegradation experiments in peer-reviewed journals
This database includes publications from 51 journals. Figure 5 shows the journals which have published at least 2 microbial defluorination studies (18 journals met the thresholds). Figure 5 summarizes the relative importance of different journals in the microbial fluorinated compound biodegradation field. By numbers of citations, Environmental Science & Technology (ES&T) ranks highest. By number of articles, Applied and Environmental Microbiology and Biodegradation are tied for the highest rank. By h-index, Applied and Environmental Microbiology, Biodegradation, and Science of the Total Environmental (STOTEM) have an equivalently high rating.
Table 2
Top ten most highly cited publications on microbial degradation of fluorinated compounds. The number of citations was retrieved from SCOPUS bibliographic data in May 2023.
Title | Year | Times cited | Journal | Authors |
Validation of effective roles of non-electroactive microbes on recalcitrant contaminant degradation in bioelectrochemical systems | 2013 | 317 | Environment International | Liu J.; Mejia Avendaño S. |
Biodegradation of perfluorinated compounds | 2008 | 210 | Reviews of Environmental Contamination and Toxicology | Parsons J.R.; Sáez M.; Dolfing J.; de Voogt P. |
Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2 | 1998 | 179 | Environmental Science & Technology | Key B.D.; Howell R.D.; Criddle C.S. |
Microbial dehalogenation | 2001 | 161 | Current Opinion in Biotechnology | Janssen D.B.; Oppentocht J.E.; Poelarends G.J. |
Natural attenuation and enhanced bioremediation of organic contaminants in groundwater | 2005 | 158 | Current Opinion in Biotechnology | Scow K.M.; Hicks K.A. |
Humin as an electron mediator for microbial reductive dehalogenation | 2012 | 120 | Environmental Science & Technology | Zhang C.; Katayama A. |
Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics | 2017 | 118 | Science of the Total Environment | Alexandrino D.A.M.; Mucha A.P.; Almeida C.M.; Gao W.; Jia Z.; Carvalho M.F. |
Investigating the biodegradability of perfluorooctanoic acid | 2010 | 107 | Chemosphere | Liou J.S.-C.; Szostek B.; DeRito C.M.; Madsen E.L. |
Organohalide respiring bacteria and reductive dehalogenases: Key tools in organohalide bioremediation | 2016 | 105 | Frontiers in Microbiology | Jugder B.-E.; Ertan H.; Bohl S.; Lee M.; Marquis C.P.; Manefield M. |
Degradation and defluorination of 6:2 fluorotelomer sulfonamidoalkyl betaine and 6:2 fluorotelomer sulfonate by Gordonia sp. strain NB4-1Y under sulfur-limiting conditions | 2019 | 92 | Science of the Total Environment | Shaw D.M.J.; Munoz G.; Bottos E.M.; Duy S.V.; Sauvé S.; Liu J.; Van Hamme J.D. |
Of the 51 journals with publications in this field, 4 are not bibliographically coupled to the others (Fig. 5). In this case we define bibliographic coupling as whether a journal contains articles that cite articles in another journal. By zooming in upon the 47 bibliographically coupled journals we generated Fig. 5B. When a time scale is overlayed upon the network visualization of journals publishing microbial fluorinated compound biodegradation articles (Fig. 5) it becomes evident that Hayati Journal of Biosciences, Journal of Hazardous Materials, Microbial Technology, Microorganisms, Environmental Pollution, and Science of the Total Environment journal have the most recent publications.
2.6 Analysis of authorship and collaboration in the field of microbial fluorinated compound biodegradation
In the database from this study, 105 documents were included containing a total of 409 authors. Only 60 authors are listed as publishing more than one paper in this field. Figure 6A depicts the most prolific authors in this field by number of published articles. Importantly, the first paper by any of the most prolific authors does not appear until 2013, even though articles in this database date back to 1990. This reveals the true nascency of the field.
To further investigate how collaboration occurs in the microbial fluorinated compound biodegradation field, we generated network visualization maps based on co-authorship among authors with at least three publications in this field (Fig. 6B). These authors are well established, and their collaborations may signify greater advances in the field than collaborations among authors with only one publication. On the collaboration map (Fig. 6B), there are 24 authors split into nine clusters. The largest cluster (red) contains 9 authors from institutions in China. The second largest clusters consists of 4 authors from institutions in Portugal. All other clusters contain less than 4 authors. Interestingly there were 5 authors which did not collaborate with other authors with at least three publications in the microbial defluorination field. While it is clear from Fig. 6B that there is significant collaboration between disproportionately high producing authors in the field of microbial defluorination, further collaboration between the smaller clusters and isolated authors could hasten the proliferation of foundational knowledge in this field.
This study demonstrates that much research has accrued in the field of microbial fluorinated compound biotransformation. However, significant challenges remain in this field in order to generate biotechnologies capable of remediating fluorinated compound contaminated sites or waste streams. Some challenges apparent from this analysis include identification of microbes of capable of microbial defluorination, tracing biotransformation pathways, achieving accurate mass balances, identifying important enzymes, and further clarifying the structure dependent nature of fluorinated compound biotransformation. These challenges could be addressed in future research in a comprehensive manner.