Mapping Research on Microbial Remediation of Metals in Soil (2020–2025)

Abstract

This study involved a systematic literature review using bibliometric analysis to examine the evolution and current trends of Biological Remediation studies. The bibliometric analysis was used for the descriptive, intellectual, social, and conceptual network analyses, while systematic reviews were used to identify the application of the Biological Remediation. A total of 4835 papers were selected and extracted from Scopus between 2020 and 2025. The publication trends, most influential countries and articles, leading journals, collaboration networks, coupling networks, and application of the Biological Remediation in various disciplines were described. This study summarized the research agenda of the Biological Remediation field, which would be helpful for researchers and funding agencies. This article highlights four new research directions in Current Bioremediation Trends: (1) understanding the interactions between petroleum hydrocarbons and heavy metals in composite pollution systems; (2) exploring microbial community succession during bioremediation; (3) utilizing biosurfactants to enhance contaminant solubilization and biodegradation; and (4) developing integrative, multi-mechanistic remediation approaches.

1. Introduction

Heavy metal contamination in soils has become an increasing environmental issue worldwide, particularly in regions undergoing rapid industrialization, intensive agriculture, and extensive mining [1,2]. Activities such as improper disposal of industrial effluents, overuse of agrochemicals, and unregulated mining operations contribute significantly to the accumulation of toxic metals such as cadmium (Cd), lead (Pb), arsenic (As), chromium (Cr), and mercury (Hg) in terrestrial ecosystems [3,4,5,6]. These metals are non-biodegradable and can persist in the environment for extended periods, posing severe risks to human health and ecological stability [7]. Their presence in soil negatively affects microbial activity, plant growth, and soil physicochemical properties, thereby impairing overall soil quality and fertility [8]. In response to these threats, biological remediation leveraging the metabolic, sorptive, and transformative capacities of microorganisms, plants, or their consortia has emerged as a promising, sustainable alternative to conventional physicochemical cleanup methods. Microbes can immobilize, transform, or even detoxify metals via processes like biosorption, bioaccumulation, redox transformations, and by mediating plant–microbe interactions that enhance phytoextraction or phytostabilization [3,9,10].

Biological remediation, using microbes and plant–microbe systems, offers an eco-friendly and cost-effective alternative to chemical or physical cleanup methods. Bioremediation has emerged as a viable, environmentally sustainable alternative to conventional remediation techniques, such as soil excavation, washing, or chemical stabilization, which are often costly, energy-intensive, and potentially disruptive to soil structure and function [11,12,13,14]. Biological approaches harness the natural detoxification capabilities of microorganisms, including bacteria, fungi, and archaea, as well as plant–microbe consortia, to degrade, transform, or immobilize contaminants in situ [15]. These systems can be applied under a range of environmental conditions with minimal disturbance to native ecosystems. Their relatively low operational costs and ability to restore soil functionality make them particularly attractive for long-term remediation strategies, especially in resource-limited settings or in large-scale contaminated sites [16,17,18].

Microorganisms can detoxify or immobilize metals via biosorption, bioaccumulation, redox reactions, and by facilitating plant uptake or stabilization. Microorganisms employ a range of metabolic and physicochemical processes to interact with heavy metals and mitigate their toxicity in soils [19,20]. Biosorption involves the passive binding of metal ions to cell surface functional groups, while bioaccumulation entails the active uptake and intracellular storage of metals. In addition, many microbes possess enzymatic systems that mediate redox reactions, altering the valence state of metals to less toxic or less mobile forms. Some microorganisms also enhance phytoremediation by promoting plant growth, increasing metal uptake or root stabilization through the production of chelating agents (e.g., siderophores), organic acids, or phytohormones [21,22,23]. These mechanisms collectively contribute to the detoxification, immobilization, or transformation of metals in contaminated soils, thereby supporting biogeochemical cycling and ecological restoration [24,25,26].

Although the field of microbial remediation has seen substantial research activity in recent years, there is a lack of a comprehensive synthesis that integrates the key findings, methodological advancements, and emerging directions from 2020 to 2025. Most existing studies are case-specific or geographically localized, often focusing on individual microbial strains or remediation scenarios. This fragmentation hinders the development of generalized principles or scalable models for field application. Moreover, rapid developments in microbial ecology, genomics, and bioinformatics have created a dynamic research landscape, necessitating periodic reviews that can distill high-impact contributions and guide future investigations. Addressing this gap through systematic evidence synthesis is critical for evaluating the maturity of the field and identifying bottlenecks in knowledge or technology transfer. While multiple case studies and experimental findings have demonstrated the efficacy of microbe-assisted and plant–microbe joint remediation, the broader trends, knowledge gaps, and emerging frontiers in this field over the recent period (2020–2025) remain only partially synthesized [27,28,29,30,31]. Aspects such as which microbial taxa are most studied, which soil–metal contexts are best addressed, what scales (lab vs. field) are dominating, and how research collaborations, geographical focus, and methodological approaches are evolving have received fragmented attention.

Bibliometric analysis helps identify trends, key contributors, collaboration networks, and research gaps in the field. Bibliometric analysis has become a widely used method for quantitatively evaluating scientific research output and impact [32,33,34,35]. By analyzing publication metadata such as authorship, citations, keywords, institutional affiliations, and journal sources, bibliometrics can reveal temporal trends, thematic evolution, influential publications, and leading contributors in a given field. It also highlights patterns of international collaboration and cross-disciplinary integration, offering insights into how research communities are structured and how knowledge is disseminated. When applied to microbial bioremediation, bibliometric methods can help uncover underexplored subfields, emerging hotspots, and the degree of translation from laboratory research to practical application, thereby informing strategic planning for researchers, funding agencies, and policymakers [36,37,38].

A combined bibliometric and systematic review approach can provide a comprehensive picture of both the scientific landscape and the practical effectiveness of remediation strategies. Integrating bibliometric analysis with systematic review methodologies allows for a holistic assessment of a research domain, combining quantitative insights into publication trends with qualitative synthesis of experimental evidence. This dual approach offers a more nuanced understanding of both the intellectual structure and technological maturity of microbial bioremediation [37,39]. Over the past decade, a surge in research has focused on harnessing microbial processes to immobilize, transform, or remove heavy metals from contaminated soils. However, despite the expanding body of literature, there remains a need for a comprehensive synthesis that maps research trends, identifies influential contributions, and clarifies the evolution of key themes in the field. This study addresses this gap by integrating bibliometric analysis with systematic evidence to evaluate global research on microbial remediation of heavy metal-contaminated soils between 2020 and 2025.

This study aims to deliver a structured and evidence-based overview of biological remediation research between 2020 and 2025, with a focus on highlighting emerging themes, influential publications, and research hotspots through bibliometric mapping. These insights are intended to support future innovation, cross-sector collaboration, and more effective deployment of microbial bioremediation technologies at scale.

2. Materials and Methods

This section describes the details of the proposed methodology used for this study. The proposed methodology consists of three significant steps: data collection, integration, and analysis and synthesis of results. To analyze the research trends, keywords and content analysis, etc., of biological remediation research, VOSviewer 1.6.20 and Biblioshiny 4.5.1 software were used.

2.1. Research Data Collection Methodology on Biological Remediation Research

The research data were collected on Scopus as it is an appropriate search engine containing primary citation sources and publishes peer-reviewed journals and conferences. The data collection process was completed on 4 September 2025. The keywords utilized to collect information on biological remediation research are shown in Table 1. Search step 1 in Table 1 shows the keywords searched on the Scopus search engine, and search step 2 indicates that data collection was limited to 2020 to 2025. Search step 3 only displays articles in English. The final collection of most relevant documents on biological remediation research included 4835 articles.

Table 1. Data collection steps in Scopus.

Search Steps	Query on Scopus	Description	Number of Documents
1	TITLE-ABS-KEY	((soil OR “agricultural soil*” OR topsoil OR subsoil OR rhizosphere OR “mine* tailing*” OR “industrial site*” OR brownfield*) AND (“heavy metal*” OR “toxic metal*” OR metalloid* OR as OR cd OR pb OR hg OR cr OR ni OR cu OR zn OR sb) AND (microb* OR bacteri* OR fungi OR fungal OR “arbuscular mycorrhizal” OR amf OR actinomycet* OR microalga*) AND (bioremediat* OR biosorpt* OR bioaccumulat* OR bioleach* OR biominerali* OR “microbial-induced carbonate precipitation” OR micp OR “microbial-induced phosphate precipitation” OR mipp OR “microbial-induced sulfide precipitation” OR misp OR bioaugment* OR rhizoremediat* OR “bacteria-assisted phytoremediation” OR “microbe-assisted phytoremediation”))	10,528
2	LIMIT-TO PUBYEAR	2020–2025	6215
3	Language	English	4835 papers

2.2. Data Integration

This study integrates datasets obtained from multiple search engines to provide a comprehensive and unified overview. The following section outlines the data integration procedure. Two main approaches can be used for combining bibliometric data: through the R package 4.5.1 or Microsoft Excel.

In this work, Excel was selected due to its several advantages, particularly its ability to retain non-standard data fields (unique column tags), which are essential for maintaining data completeness during bibliometric analysis. Conversely, the R package offers a more automated and efficient integration process for datasets that share identical structures; however, it omits uncommon columns and merges only those with matching tags. The R-based data integration method can be implemented using the following commands:

library (RefManageR)

> scopus = convert2df(file. choose(), dbsource = “scopus”, format = “bibtex”)

> > mergedSources = mergeDbSources(scopus,remove.duplicated = TRUE)

> writexlsx(Coverteddata, “Path..”)

In the present study, data from the Scopus database were integrated using both Biblioshiny and Excel. Biblioshiny is a web-based interface built within the Bibliometrix 5.0 package, combining the analytical functions of Bibliometrix with the user-friendly features of the Shiny environment. Its main advantage is accessibility for users without programming experience.

The datasets were first imported into Biblioshiny from each database and subsequently exported to Excel for merging. The integration process in Excel followed these steps:

• Open a new Excel workbook.
• Navigate to the Data tab → select Get Data → and then Launch Power Query Editor.
• In the Power Query window, choose New Source → File → Excel Workbook, and open the first file.
• Repeat the import process for all remaining files to compile the complete dataset.

2.3. Analysis and Synthesis of Results

After retrieving and extracting relevant publications from the Scopus database, bibliometric techniques were employed to obtain the information necessary to address the research objectives. Subsequently, analyses were conducted using Biblioshiny (an R-based interface) and VOSviewer to examine the key aspects identified in the research questions.

Biblioshiny, developed within the Bibliometrix R package by Aria and Cuccurullo [40] serves as a widely recognized quantitative tool for scientometric and bibliometric investigations. It is particularly advantageous for users without programming expertise, as it allows the generation of comprehensive statistical summaries directly from bibliographic datasets.

In contrast, VOSviewer, introduced by van Eck and Waltman [41], is a specialized software designed to construct and visualize bibliometric networks—such as co-occurrence maps of keywords, countries, authors, and journals. Although both tools contribute to bibliometric analysis, they serve complementary purposes: Biblioshiny is well-suited for general statistical exploration, while VOSviewer excels in creating visual network maps that illustrate relationships among selected elements, thereby facilitating easier interpretation of research patterns

3. Results

3.1. Descriptive Analysis

This subsection provides a comprehensive overview of publication and citation trends in the field of biological remediation, identifying the most productive countries, leading journals, and highly cited publications to reveal major research patterns and key sources shaping this domain.

The bibliometric data on biological remediation, retrieved from the Scopus database, are summarized in Table 2. The dataset comprises 4835 documents published between 2020 and 2025 across 854 different sources. These publications exhibit an average age of 2.38 years, an average of 15.81 citations per article, and an annual growth rate of 2.04%. Collectively, the sources in this field reference 6708 cited works.

Table 2. Key evidence of the biological remediation review from the Scopus database.

Description	Results
Timespan	2020:2025
Sources (Journals, Books, etc.)	854
Documents	4835
Annual Growth Rate %	2.04
Document Average Age	2.38
Average citations per doc	15,61
References	32,132
Document Contents
Keywords Plus (ID)	17,602
Author’s Keywords (DE)	23,391
Authors
Authors	18,978
Authors of single-authored docs	90
Authors collaboration
Single-authored docs	112
Coauthors per doc	5.34
International coauthorships %	26.06
Document Types
Article	3264
Book	22
Book chapter	725
Conference paper	207
Conference review	12
Data paper	1
Editorial	2
Erratum	5
Letter	2
Note	12
Review	577
Short survey	6

The dataset includes 3264 research articles, 725 book chapters, 207 conference papers, five erratum papers, and 577 review papers. Moreover, the 268 biological remediation documents analyzed contain 17,602 indexed keywords (or Keywords Plus), 23,391 author keywords, 18,987 contributing authors, and 32,132 total references. Among the retrieved publications, 112 papers were authored by a single researcher, and 26.06% involved international coauthorship, indicating a moderate degree of global scientific collaboration in this research field.

3.2. Annual Scientific Publication, Citation Trends and Subject Areas

This section presents a detailed analysis of publication and citation trends related to research on Microbe–Metal–Soil interactions and biological remediation from 2020 to 2025. As illustrated in Figure 1a, both the number of publications and citations in this research domain show a generally increasing trend over the study period, with an average annual growth rate of 10.48%. According to Figure 1a, research output in 2020 was relatively modest, with 632 published articles. A notable increase occurred in subsequent years, peaking in 2022, before experiencing a significant decline to 74 publications in 2023. The highest number of articles within the five-year period was recorded in 2024, indicating a resurgence in research interest.

Figure 1. (a) Subject area and (b) publications and citations trend related to Microbe–Metal–Soil interactions and biological remediation were generated using Microsoft Excel, based on data collected over the period 2020–2025.

The topic of bioremediation research has been discussed in 32 disciplines, with the top 10 displayed in Figure 1b. The highest number of publications was recorded in Environmental Science 29% (n = 2508), highlighting its dominant role in this research area. This was followed by Agricultural and Biological Sciences, 14% (n = 1196) and Immunology and Microbiology, 10% (n = 887), indicating significant contributions from disciplines focusing on biological and ecological processes. Biochemistry, Genetics and Molecular Biology (n = 812) and Engineering (n = 802) also showed substantial involvement, reflecting the growing integration of molecular and technological approaches in environmental research. Moderate contributions were observed from Medicine (n = 623), Earth and Planetary Sciences (n = 557), and Chemical Engineering (n = 484), while fewer publications were associated with Chemistry (n = 423) and Energy (n = 271). Overall, the data suggest that environmental and life sciences form the core foundation of research in this field, complemented by important interdisciplinary input from engineering and physical sciences.

The analysis indicates a growing academic interest in biological remediation research over the past several years, with a notable peak in 2024, during which a total of 1023 articles were published, the highest within the study period. Although there was a decline in the number of publications after 2024, the overall trend remained positive up to 2020. The noticeable drop in scientific output observed in 2025 is attributed to the limited data collection period, which only includes publications indexed up to September 2025. As a result, the number of articles published and indexed in Scopus for 2025 remains low and is not fully representative of the entire year.

Citation trends for biological remediation research varied throughout the observed period. The highest number of citations was recorded in 2020, reaching 20,182 citations, likely due to the continued reliance on foundational studies during the early phase of growth in this research domain. In contrast, 2025 saw the lowest citation count, which can be attributed to the shorter data collection window ending in April 2025. It is anticipated that citation counts for 2025 will increase over time as more articles accumulate citations.

Table 3 presents the annual number of published articles, the average total citations per article, the average total citations per year, and the corresponding citation years.

Table 3. Annual Publication Metrics for Biological Remediation Research (2020–2025).

Year	Number	MTCPY	MTCPA	Citable Year
2020	632	5.32	31.93	5
2021	727	5.18	25.89	4
2022	914	5.10	20.40	3
2023	840	4.64	13.91	2
2024	1023	2.58	5.15	1
2025	699	1.26	1.26	0

Note: MTCPY—Mean Total Citations Per Year; MTCPA—Mean Total Citations per Article.

3.3. Most Productive Journals in Biological Remediation Research

Academic journals serve as essential platforms for disseminating innovative research and advancing knowledge. Identifying the most prolific journals in the field of biological remediation is therefore crucial for understanding where high-impact research is being published. These journals play a key role in shaping the field by rigorously peer-reviewing manuscripts and publishing high-quality studies that contribute to the latest scientific developments.

In this study, a total of 4835 journal articles related to biological remediation were published across 153 different journals. Figure 2 highlights the top 10 most influential journals in this domain, ranked by the number of publications. Together, these ten journals account for 1040 articles, representing 21.50% of all publications analyzed. Journal of Hazardous Materials emerged as the most productive journal, publishing 186 articles, followed by Science of the Total Environment with 172 articles, and Chemosphere with 135 articles.

Figure 2. The top ten leading journals.

The citation counts for each journal are presented in Table 4, along with their average citations per article. For instance, the Journal of Hazardous Materials accumulated 5721 citations, ranking first overall, followed by Chemosphere with 4657 and Science of the Total Environment with 4533 citations. However, because citation counts varied widely across different journals, some journals achieved higher averages despite lower total citations. Notably, Frontiers in Microbiology, Ecotoxicology and Environmental Safety, and Chemosphere demonstrated the highest average citations, at 39.41, 34.49, and 34.48 citations per article, respectively.

Table 4. Key metrics and impact indicators of the top 10 productive journals.

№	Name	PSY	TP	TC	AC	IF	H Index
1	Journal of Hazardous Materials	1975	186	5721	30.85	13.6	375
2	Science of the Total Environment	1972	172	4533	26.35	7.963	353
3	Chemosphere	1972	135	4657	34.49	8.7	305
4	Environmental Science and Pollution Research	1994	96	1658	17.27	5.8	212
5	Environmental Pollution	1970	92	2424	26.34	8.88	328
6	Frontiers in Microbiology	2012	91	3587	39.41	4.5	259
7	Ecotoxicology and Environmental Safety	1977	72	2267	34.48	6.3	197
8	Journal of Environmental Management	1973	69	1667	24.15	9.84	268
9	Microorganisms	2013	67	1180	17.6	4.6	87
10	Scientific Reports	2011	60	751	12.51	4.08	347

Note: PSY—Starting Year of Publication; TP—Total Publication; TC—Total Citations; AC—Average Citations; IF—Impact factor, H index—Hirsch index.

In terms of impact factor, the Journal of Hazardous Materials reported the highest value at 13.6 for the 2023–2024 period. It is followed by the Journal of Environmental Management with an impact factor of 9.84, and Environmental Pollution with an impact factor of 8.88. These metrics underscore the significant influence of these journals in the field of biological remediation.

The h-index, which quantifies both the productivity and citation impact of a journal’s publications, provides further insight into its influence. The h-index for the Journal of Hazardous Materials is 375, indicating that 375 of its articles have each been cited at least 375 times. Other notable journals include Science of the Total Environment with an h-index of 317, Scientific Reports with an h-index of 347, and Environmental Pollution with an h-index of 328. These values reflect the sustained impact and relevance of these journals in advancing research on biological remediation, sustainable environmental management, microbiology, soil science, ecology, engineering and environmental biotechnology.

3.4. Most Influential Articles in Biological Remediation Research

Analyzing the highly cited works offers valuable insights into prevailing trends and guiding directions in biological remediation. Table 5 lists the top ten most cited articles published in the domain during the period studied. Total citation counts provide one measure of impact, as articles with higher citation numbers tend to be more recognized in the field. Among the 4835 articles surveyed, the review “Polycyclic Aromatic Hydrocarbons: Sources, Toxicity, and Remediation Approaches” by Patel [42] stands out with the highest number of citations—921. The second most cited article is “Metal Contamination and Bioremediation of Agricultural Soils for Food Safety and Sustainability” by Hou [43], which garnered 861 citations and an average citation rate of 172.2. The third is “Current Status of Pesticide Effects on Environment, Human Health and its Eco-Friendly Management as Bioremediation: A Comprehensive Review” with 681 citations by Pathak [44].

Table 5. The leading ten most referenced articles.

Rank	TC	AC	Article Title	References	Journal Title
1	921	184.2	Polycyclic Aromatic Hydrocarbons: Sources, Toxicity, and Remediation Approaches	[42]	Frontiers in Microbiology
2	861	172.2	Metal contamination and bioremediation of agricultural soils for food safety and sustainability	[43]	Nature Reviews Earth and Environment
3	681	227	Current status of pesticide effects on environment, human health and its eco- friendly management as bioremediation: A comprehensive review	[44]	Frontiers in Microbiology
4	420	210	Heavy Metal Contamination in Agricultural Soil: Environmental Pollutants Affecting Crop Health	[45]	Agronomy
5	379	94.75	Rhizosphere bacteria in plant growth promotion, biocontrol, and bioremediation of contaminated sites: A comprehensive review of effects and mechanisms	[46]	International Journal of Molecular Sciences
6	360	120	Recent advances in soil remediation technology for heavy metal contaminated sites: A critical review	[47]	Science of the Total Environment
7	336	67.2	Factors affecting the performance of microbial-induced carbonate precipitation (MICP) treated soil: a review	[48]	Environmental Earth Sciences
8	254	84.7	Biodegradation of microplastics: Better late than never	[49]	Chemosphere
9	250	50	Bio-remediation of desiccation cracking in clayey soils through microbially induced calcite precipitation (MICP)	[50]	Engineering Geology
10	240	80	Interactions between microplastics and soil fauna: A critical review	[51]	Critical Reviews in Environmental Science and Technology

3.5. Influential Authors, Their Affiliations, and Countries

Understanding who the key researchers are—and where they are based—is especially valuable for early-career scientists. There are multiple ways to stay current on their work: for instance, Google Scholar offers email alerts when these authors publish new articles, and social platforms such as ResearchGate or LinkedIn provide further engagement opportunities.

Figure 3 highlights the most influential authors in the field of biological remediation. It displays both their total publication counts and their fractional authorship contributions. Fractional authorship is used to assess an author’s proportional contribution to coauthored papers, under the assumption that all coauthors contributed equally. It is calculated as:

Frac Freq = TNA/h

where TNA is the number of articles coauthored by that individual, and h is the number of coauthors per article.

Figure 3. Total publications and fractional authorship contribution of the top 10 influential authors.

The analysis of author productivity and impact (Figure 4) indicates that publication counts among the top ten contributors range from 15 to 20 articles. Tang C.S. and Kawasaki S. lead with 20 publications each, while Bhatt P. demonstrates the highest citation impact (1365 citations) despite a slightly lower output (19 articles). Citation counts vary substantially, from 166 to 1365, reflecting differences in research influence and visibility. Authors such as Chu J. (936 citations) and Tang C.S. (1319 citations) show high citation rates per publication, indicating strong research impact, whereas others (e.g., Montoya B.M.) exhibit lower citation frequencies, potentially due to recent publications or narrower research scope. Finally, Cheng Liang produced 15 articles with a total of 382 citations, rounding out the top ten authors.

Figure 4. Top 10 authors’ production over time.

Regarding the institutions most frequently represented among corresponding authors, the Ministry of Education of the People`s Republic of China occupies the leading position, followed by the Chinese Academy of Sciences, as illustrated in Figure 5.

Figure 5. Most relevant institutional affiliations.

Figure 6 displays the number of publications attributed to each country, which is determined by the affiliation of the corresponding authors. In this analysis, the total article count per country reflects the frequency of publications. Additionally, we evaluate International Authorship (IA), defined as the proportion of publications in which at least one coauthor is affiliated with a country different from the corresponding author’s country.

Figure 6. Number of articles based on Corresponding author, International- Multiple Countries Publications, Same country—Single Country Publications.

Country scientific production measures how often a country appears in authors’ affiliations across all articles. For instance, if a paper lists authors from the United States, China, and India, then each of those countries gets one “count” for that article. Hence, each article contributes as many counts as there are countries represented. As a result, the summed values of country production typically exceed the number of articles in the dataset. In our analysis, China leads in the number of published articles, followed by India and the United States.

3.6. Most Productive Countries

A total of 113 countries contributed to research in biological remediation. Figure 7 lists the top 10 most prolific nations. China leads with 1499 publications, followed by India with 1313, and the United States with 384. In terms of citations, China also ranks first (33,923 total citations), with India in second place (14,803), and Pakistan third (2625).

Figure 7. Leading countries by the number of publications, total citations received, and average citations per paper. Note: TP—Total Publication; TC—Total Citations; AC—Average Citations.

In assessing citation impact, citations are frequently used as a proxy for research quality. As illustrated in Figure 7, China leads with 33,923 total citations and an average of 22.63 citations per article. Notably, the United Kingdom also performs well, placing second in total citations (2625) and with an average of 14.11 citations per article, despite having fewer publications than India and the United States.

Furthermore, there is a clear correlation between national scientific production and changes in country-level output over time. Figure 8 charts the publishing trends of the ten most productive countries. Between approximately 2020–2021, the average annual output per country remained under 300 articles; after 2021, however, there was a marked increase—especially in China, India, and the United States

Figure 8. Network analysis of countries’ coauthorships, weighted by the number of documents.

3.7. Network Visualization

Network visualization provides a graphical representation of relationships in bibliometric data—such as country-level coauthorships, keyword co-occurrences (co-words), and bibliographic coupling. It enables researchers to see how collaboration, concept co-occurrence, and shared citation patterns shape the structure of a field. Nodes typically represent entities (authors, countries, or keywords), while node size reflects quantity (such as number of publications or keyword frequency). The colors of nodes often denote different clusters or communities, and the thickness of edges (lines connecting nodes) indicates the strength of the relationships.

3.7.1. Coauthorship Among Countries

Analysis of country coauthorship examines the strength of collaborations among nations, offering researchers insight into how countries contribute collectively to the biological remediation field. In this study, countries were included in the network analysis only if they had contributed at least ten publications. Out of 61 countries initially identified, 35 were excluded because they had no coauthorship ties with other countries under this threshold. The top ten most collaborative countries, ranked by total link strength, are shown in Table 6. Here, total link strength refers to the number of articles coauthored by researchers from different countries—in other words, countries that collaborate more widely will tend to display higher link strengths.

Table 6. Countries Coauthorship.

№	Country	TA	Link	TLS
1	China	1496	56	722
2	India	1313	60	562
3	United States	387	52	465
4	Saudia Arabia	148	39	274
5	Pakistan	186	40	262
6	Malaysia	118	39	194
7	Australia	118	39	190
8	South Korea	129	36	168
9	United Kingdom	127	40	168
10	Egypt	110	37	147

Note: TA refers to the total article, while TLS is total link strength.

Since China leads in publication output in the field of bioremediation, it is unsurprising that it also exhibits the highest total link strength (722) in international coauthorship networks. India follows, with a total link strength of 562 corresponding to its second-highest publication count (1313). In general, the coauthorship analysis suggests that more developed countries (e.g., China, the USA) tend to engage more actively in cross-national collaborations than developing nations such as Egypt. Figure 8 provides a number of publications, collaboration clusters and strength of links of country coauthorship in bioremediation research.

These countries were grouped into eight primary clusters, each represented by a distinct color: red, green, blue, dark yellow, violet, light blue, orange, and brown. Below are the details for the top five clusters that have the greatest number of constituent countries.

Based on node size in Figure 9, the most central or influential country in each cluster (in terms of publication output in bioremediation research) are: Iran (Cluster 1), Spain (Cluster 2), United Kingdom (Cluster 3), Singapore (Cluster 4), India (Cluster 5), China (Cluster 6), Germany (Cluster 7), and Israel (Cluster 8).

Figure 9. A network analysis of keyword co-occurrence.

3.7.2. Keywords Co-Occurrence Analysis

Keyword co-occurrence analysis is a widely used technique in bibliometric studies, as it helps uncover central research topics and thematic structures [40]. In this study, we analyzed a pool of 23,434 keywords to map the prevailing research hotspots in bioremediation. To focus on the most significant terms, we imposed a minimum occurrence threshold of ten, reducing the set to 50 keywords for visualization.

Keywords that lacked any connections to others were excluded from the network. Table 7 lists the top 10 author keywords, ranked by total link strength. “Bioremediation” led with a total link strength of 21,272, followed by “Nonhuman” (16,914) and “Soil pollution” (15,712). These three terms also emerged as the most frequent in the descriptive analysis (Table 8), reinforcing their centrality in the research field.

Table 7. Keyword Co-Occurrence Analysis.

№	Keywords	Occurences	Link	TLS
1	Bioremediation	2645	49	21,272
2	Nonhuman	1293	42	16,914
3	Soil pollution	1403	38	15,712
4	Article	1172	33	15,686
5	Soil	1144	30	14,366
6	Soil pollutant	918	25	13,779
7	Soil pollutants	910	21	13,664
8	Biodegradation, environmental	960	20	13,483
9	Controlled study	808	18	11,247
10	Bacteria	1039	15	11,197

Table 8. Primary Clusters of Keywords Co-Occurrence.

Cluster	Keywords	Colour
1	Article, bacterial strain, concentration, controlled study, enzyme activity, microbial community, microbial diversity, nonhuman, pH, physical chemistry, proteobacteria, RNA 16s, scanning electron microscopy, soil microflora, unclassified drug	Red
2	Bioaccumulation, biochemistry, biomass, cadmium, heavy metal, heavy metals, human, lead, metals, heavy, phytoremediation, plant growth, rhizosphere, toxicity	Green
3	Bacteria, microorganism, biodegradation, bioremediation, biotechnology, contaminated soils, contamination, degradation, microbial activity, soil pollution, soil remediation, soils	Blue
4	Bacterium, biodegradation environmental, chemistry, genetics, metabolism, microbiology, soil, soil microbiology, soil pollutants, soil pollutant	Purple

Simultaneously, the co-occurrence of author keywords was visualized via a network map (Figure 9). In this visualization, node size corresponds to the frequency of each keyword in the bioremediation literature, while node color reflects cluster membership.

The keywords were grouped into four principal clusters, with links drawn between terms that co-occur in the same publications—terms sharing the same color appear in the same cluster. In our analysis, many keywords were associated with biotechnology and environmental pollution. Detailed compositions of the four clusters are provided in Table 8.

Of all the keywords, “Bioremediation” exhibits the highest node frequency and thus appears as the largest node in the network. The connection (edge) between nodes represents the likelihood that two keywords co-occur in an article. Notably, “Bioremediation” has the highest number of links, being associated with 49 other keywords.

3.8. Bibliographic Coupling

Originally introduced by [43] bibliographic coupling is a method for identifying the similarity between documents based on shared references [42]. It serves as an important tool in bibliometric analysis to assess the relatedness of entities such as countries or publications. In this study, bibliographic coupling was applied to both countries and articles within the bioremediation research domain.

3.8.1. Countries

Bibliographic coupling among countries occurs when publications from two or more countries cite the same references. This analysis reveals the degree of similarity in research focus or intellectual foundations between nations. The visualization of bibliographic coupling is shown in Figure 10, where node size represents a country’s publication volume and color denotes cluster membership.

Figure 10. Bibliographic coupling of countries.

Out of 67 countries, 37 met the minimum threshold of 10 documents for inclusion. As in Table 2, the coupling analysis identified China, India, and the United States as the top three contributors to bioremediation research. Six clusters were identified, each represented by a distinct color (red, green, blue, yellow, violet, and light blue). India leads the largest cluster (red), showing strong coupling with the USA and China. China heads the green cluster and is closely coupled with Singapore and Japan. The blue cluster is led by Malaysia, coupled with Indonesia and South Africa. Thailand anchors the yellow cluster, forming strong ties with France and Vietnam. Chile leads the fifth cluster, actively coupled with South Korea.

In the bibliographic coupling network, India occupies a central position, demonstrating significant influence in the bioremediation research field by virtue of its strong coupling links with many other countries.

3.8.2. Articles

Bibliographic coupling between publications occurs when two papers cite one or more of the same references, thereby revealing thematic similarity in their content. In this analysis, nodes in the visualization are colored to reflect clusters of related research topics, while node size corresponds to the total number of citations each paper has received. Figure 11 illustrates the bibliographic coupling network for bioremediation studies, restricted to papers that have attained at least ten citations. A total of 1837 articles met this threshold and are interconnected in the network, indicating substantial thematic overlap among them.

Figure 11. Bibliographic coupling of publications. Date from [15,26,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66].

The bioremediation research publications were divided into three clusters, each represented by a different node color: red, green, and blue. The blue cluster is positioned significantly apart from the red and green clusters. Because articles that share similar references are grouped by the same node color, the articles in the blue cluster are distinct from those in the other two clusters.

The red cluster is the largest, containing 19 publications with a total of 1357 citations, averaging 71.4 citations per article. Most publications in this cluster focus on environmental earth sciences, geotechnical and geoenvironmental engineering, and rock mechanics. The most highly cited paper in the red cluster is by Tang [48], which examines factors influencing the performance of microbial-induced carbonate precipitation-treated soil and has received 336 citations.

The green cluster is the second largest, consisting of 16 articles. Publications in this cluster have garnered a total of 714 citations, averaging 44.6 citations per article. Research in this cluster mainly centers around biomimetics, nanobiomaterials, engineering geology, environmental research, geomechanics related to energy and the environment, and biotechnology. A smaller portion of the publications also addresses earth science and civil engineering topics. The most cited article here, by Nafisi [53], focuses on the shear strength envelopes of biocemented sands with varying particle sizes and cementation levels, with 134 citations.

The blue cluster, representing the third-largest group, comprises 15 publications that have collectively received 959 citations, with an average of 64 citations per article. Research within this cluster predominantly addresses topics such as water, air, and soil pollution, biogeotechnics, ecological engineering, microbiology, biotechnology, and biodegradation. Notably, the most-cited publication in this cluster, authored by Jalilvand [62], investigates the removal of heavy metals through bacterial mineralization and has accrued 165 citations.

Overall, while the three clusters share overlapping research domains, the focus of individual publications varies across specific thematic areas. This convergence of diverse yet related topics underscores the multidisciplinary nature of bioremediation research and highlights its strong relevance and applicability within the fields of biotechnology and environmental engineering.

4. Hot Issues

Phytoremediation has gained significant attention from researchers both domestically and internationally in the early stages of bioremediation development due to its advantages, such as operational safety, cost-effectiveness, sustainability, and eco-friendliness [27,28]. This technology represents a group of environmental approaches that utilize plant root systems, stems, or leaves to absorb, accumulate, degrade, or immobilize pollutants present in contaminated soil, water, and air [67,68]. Phytoremediation methods are generally classified into phytostabilization, phytostimulation, phytotransformation, phytofiltration, and phytoextraction [69]. The mechanisms underlying phytoremediation mainly include direct uptake and metabolic degradation of pollutants by plants, as well as rhizosphere-based processes, with the latter being the primary mechanism for the remediation of organic contaminants [70,71].

Aboud examined how phytoremediation systems enhance hydrocarbon degradation in soils, finding that such systems increase the catabolic capacity of rhizosphere soils by modifying the functional composition of microbial communities [72]. The success of phytoremediation largely depends on selecting naturally oil-tolerant plant species and enhancing their growth potential in petroleum-contaminated soils (PCS) [73].

Although phytoremediation aligns with the principles of sustainable development, it is limited by long plant growth cycles, slow remediation rates, and dependency on environmental factors, making it less ideal as a standalone restoration method [74,75,76]. Consequently, research focus has gradually shifted toward the application of broader bioremediation technologies for actual soil contamination [28]. Over time, investigations into petroleum pollution have evolved from single-compound studies to comprehensive analyses involving total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) [77,78]. PAHs—designated as priority environmental pollutants by the U.S. Environmental Protection Agency—are key constituents of petroleum hydrocarbons and pose carcinogenic, teratogenic, and mutagenic risks to humans and other organisms [79,80]. Due to their chemical stability, low degradability, and tendency to persist in soils, PAHs represent a serious environmental and public health concern, necessitating focused remediation studies [81].

An experimental mesocosm was developed by Ambaye [82] in a biosuspension reactor for the biodegradation of PHs and the decontamination of soils. The degradation of PHs and the decontamination of contaminated soil were achieved by adding external stimulants such as nutrients, activated clay, synthetic surfactants, and long-chain rhamnolipids [82].

Biostimulation involves optimizing environmental conditions (such as temperature, pH, and nutrient levels) to promote the growth and activity of indigenous degrading microorganisms, thereby enhancing pollutant removal efficiency [83]. In contrast, bioaugmentation entails the introduction of exogenous microorganisms with high degradation capacity to achieve rapid and effective pollutant breakdown [84,85]. Another research result showed that inoculation of sorghum with the heavy metal-resistant, plant-beneficial bacterial strains consortium enhanced microbial activity, such as increasing dehydrogenase activity (DHA), reducing heavy metal bioaccumulation in roots and plants, and upregulating heavy metal bioaccumulation factor (BAF) in the rhizosphere and plant [10]. Similarly, in a study conducted by Sharma (2025), the potential of a novel Bacillus sp. SSAU-2 microbe to remove Cr (VI) by up to 83% was investigated in the presence of heavy metal contamination in various combinations Pb(II) > Fe(III) > Cu(II) > Cr(VI) > Zn(II) > Cd(II) > Hg(II) [86]. Sahlaoui found that combining bioaugmentation with microbial consortia and biostimulation via nutrient amendment resulted in the most effective treatment of heavy metal contaminated sites [87].

Microbial remediation is widely adopted due to its short processing cycle, simplicity, affordability, and absence of secondary pollution [88,89]. However, its efficiency is influenced by environmental fluctuations, and the natural degradation capability of indigenous microorganisms is often limited [90]. Moreover, introduced microbial strains may face competition with native populations, reducing their effectiveness [2]. Hence, single-method microbial remediation is not considered optimal. With continuous advancements in this field, future research on bioremediation of heavy metal-contaminated soils is expected to mature further, particularly across four main directions of development.

4.1. Research on the Composite Pollution System of Oil and Heavy Metals

Petroleum naturally contains trace amounts of heavy metals such as cadmium (Cd), lead (Pb), and mercury (Hg); therefore, hydrocarbon contamination is often accompanied by heavy metal pollution [73,79]. Numerous studies have confirmed the presence of heavy metals in oilfield and industrial soils [91]. Crude oil is particularly rich in vanadium (V) and nickel (Ni), while drilling fluids are known to contain substantial levels of Pb, chromium (Cr), zinc (Zn), Cd, and copper (Cu) [92,93].

The co-occurrence of petroleum hydrocarbons and heavy metals in soils alters the composition and stability of soil ecosystems, disrupts biodiversity, and negatively impacts ecological functions. Moreover, these contaminants can bioaccumulate through the food chain, posing severe risks to animal and human health [94,95,96]. The interaction between hydrocarbons and heavy metals affects the chemical form and bioavailability of pollutants, suppresses the activity of hydrocarbon-degrading microorganisms, and complicates remediation strategies [97,98].

Despite growing awareness of this issue, research on the bioremediation of mixed petroleum–heavy metal contamination remains limited. Further investigation is required to clarify the interaction mechanisms between these pollutants and to elucidate how heavy metal stress influences hydrocarbon biodegradation processes.

4.2. Research on the Succession of Soil Microbial Communities During Bioremediation

The degradation of petroleum hydrocarbons is typically mediated by complex microbial consortia [99,100]. Understanding changes in soil microbial diversity and activity during bioremediation is crucial for evaluating microbial function and ensuring treatment efficiency [101]. Various biotechnological approaches have been employed to analyze microbial community dynamics throughout the remediation process.

Navarro-Torre et al. [102] applied aeration and organic amendments to remediate semi-arid soils contaminated with oily sludge. Using real-time PCR, BIOLOG, and DGGE analyses, they observed that bioremediation increased bacterial abundance but reduced overall microbial diversity, leading to alterations in community composition and function. Similarly, Sun utilized 16S rRNA high-throughput sequencing to examine microbial communities in petroleum-contaminated soils (PCS) from Turkey. The dominant genera identified were closely related to known hydrocarbon-degrading taxa [103].

With the advancement of molecular biology tools, more sophisticated techniques—such as degradative enzyme activity assays, metagenomic and nucleic acid-based analyses, and phospholipid fatty acid profiling—are expected to enhance the monitoring and understanding of microbial dynamics in bioremediation systems.

4.3. Application of Biosurfactants (BS) in Bioremediation

Biosurfactants (BS) are surface-active compounds produced as secondary metabolites by various microorganisms [70,104]. These amphiphilic molecules can significantly reduce surface and interfacial tension, lower the critical micelle concentration, and enhance the surface area of hydrophobic pollutants such as hydrocarbons. Consequently, they increase pollutant solubility and bioavailability, thereby stimulating microbial growth and accelerating contaminant degradation [105].

BS possess desirable characteristics, including low toxicity, biodegradability, and high activity under extreme environmental conditions, which make them highly promising agents for the bioremediation of petroleum-contaminated soils (PCS) [106]. For instance, Książek-Trela [107] investigates when eight strains of bacteria belonging to the genus Bacillus, B. coagulans, B. amyloliquefaciens, B. laterosporus, B. licheniformis, B. mucilaginosus, B. megaterium, B. polymyxa, and B. pumilus, were exposed to a mixture of polycyclic aromatic hydrocarbons (PAHs), PAH levels were reduced by 75.5–95.5% on day 35 of the experiment.

Although numerous laboratory studies have demonstrated the beneficial effects of BS on hydrocarbon removal, some field investigations have shown inconsistent or even negative outcomes [108]. This may result from BS accumulation at the oil–water interface, which reduces contact between microorganisms and pollutants, thus inhibiting biodegradation [109]. Future studies should focus on elucidating the complex interactions among BS, microorganisms, and pollutants to optimize their application in large-scale bioremediation systems.

4.4. Application of Combined Biological Remediation Technologies

Combined remediation technology integrates two or more remediation methods to exploit their synergistic advantages and enhance overall treatment efficiency. Currently, major approaches include bio-chemical remediation and inter-organismal remediation involving plants, animals, and microorganisms [110,111]. Among these, phyto–microbial remediation and chemical oxidation–microbial remediation are the most widely used techniques for restoring heavy metal-contaminated soils [112,113].

Soil amendments can immobilize toxic elements in contaminated soils, thus contributing to remediation [91]. Using activated/engineered biochars designed to enhance sorption capacity for both heavy metals and hydrocarbons is a valuable strategy targeting mixed contamination scenarios common in brownfields. Integrating biochar application with site-specific hydrocarbon pollution is an area where evidence suggests trade-offs between strong sorption and maintaining bioavailability for biodegradation [114,115,116].

Phyto–microbial remediation leverages the cooperative interactions between plants and microorganisms to immobilize, absorb, and degrade pollutants [117]. Plant roots offer a suitable habitat for microorganisms, while root exudates enhance the bioavailability of petroleum hydrocarbons and heavy metals, promoting microbial metabolism and degradation [68,118]. In return, microorganisms stimulate root biomass production and facilitate co-metabolic processes, improving pollutant utilization efficiency [119]. For example, Xun demonstrated that inoculation with plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) enhanced the tolerance of oat plants to petroleum hydrocarbons in saline–alkali soils [120].

Chemical oxidation–microbial remediation, on the other hand, employs chemical oxidation as a pretreatment step to decrease the water solubility, mobility of heavy metals and convert nontoxic form. Important enzymes in microbial metabolism often contain sulfhydryl (SH) groups, and heavy metals such as Cd²⁺, Ag²⁺, and Hg²⁺ can bind to these groups, which inhibits the activity of metals [23].

Biological remediation has emerged as a research hotspot in the field of metal detoxification. However, discrepancies between laboratory conditions and actual field environments necessitate further in situ studies to verify its effectiveness. Overall, keyword visualization analyses in the field of metal-contaminated soil bioremediation indicate that recent research trends focus on understanding composite pollution involving heavy metals and developing strategies to enhance bioremediation efficiency. As research progresses, these studies are expected to become increasingly comprehensive and mechanistic.

5. Conclusions

This study addressed the evolution and research trend of the Biological Remediation literature between 2020 and 2025 using the bibliometric and systematic literature review. The bibliometric analysis showed significant research in the Biological Remediation research as a continuous upward trend recently.

A total of 4835 publications and over 32,000 citations over five years is a key strength of the field, while demonstrating vigorous global engagement. China and India have established themselves as leading contributors both in volume and influence, dominating not only publication counts but also citation impact and collaboration networks. However, the overwhelming concentration of publications in a handful of countries reveals a persistent geographical imbalance. Many developing and highly polluted regions where bioremediation research is urgently needed remain underrepresented in both authorship and collaboration networks. This imbalance limits the global applicability of research findings and underscores the need for more inclusive international research frameworks.

Journal analysis confirms that high-impact work is concentrated in a relatively small number of influential journals, notably Journal of Hazardous Materials, Science of the Total Environment, and Chemosphere. These journals were ranked as the top and most probable journals that can overtake bioremediation research in the near future. While these journals provide robust platforms for dissemination, the dominance of a few outlets suggests potential biases in research visibility and access, especially for early-career researchers and scientists from low-resource institutions. Similarly, the top-cited articles reveal a strong emphasis on heavy metals, pesticides, microplastics, and microbial technologies, indicating clear thematic priorities but also highlighting gaps in areas such as emerging contaminants, climate–soil–microbe interactions, nanoremediation risks, and socio-environmental impacts of bioremediation technologies.

The top three most influential articles on microbiology and environment were written by Patel, Hou and Pathak [42,43,44].

From the collaboration network, countries were divided into eight clusters: Iran, Spain, United Kingdom, Singapore, India, China, Germany, and Israel are the leading countries of every cluster in terms of published volumes. Although international coauthorship is moderate (26%), network structures show that collaboration remains highly regionalized, with China, India, and the United States forming the core of most clusters. Countries with high pollution burdens (e.g., African, Central Asian, and Latin American nations) exhibit weak linkage strengths, partly due to resource constraints, limited research funding, and lack of access to high-impact publication channels. Strengthening global research equity will require intentional capacity-building initiatives, cross-border funding schemes, and more accessible publication models.

Concurrently, “Bioremediation” is the most popular keyword used with the highest usage and link numbers. From the coupling of articles, all publications have been categorized into three clusters, while most of the clusters presented the environmental earth sciences and rock mechanics. While these foundational themes are essential, the relatively low presence of keywords related to system-level environmental assessments, sustainability metrics, or advanced computational approaches (e.g., AI-driven site modeling, metagenomic prediction tools) suggests a need for broader integration of emerging technologies and interdisciplinary frameworks. The limited appearance of terms associated with policy, regulation, or technology transfer further reflects a gap between research output and practical environmental management strategies.

This study faced some limitations, the first being the accuracy of the datasets extracted from Scopus. The datasets retrieved might be slightly different when conducting the search query on different dates, even though the exact search keywords and steps were used, as Scopus updates its list of published articles daily. For example, the search query of this study was retrieved on 24 September 2025; therefore, the search result obtained may be different, as there is a stream of Biological Remediation studies published after that time.

Second, the accuracy of results also depends on the types of sources used to extract datasets. In this study, the datasets were extracted from the Scopus database via the search process. However, using a single scientific database, the high-quality Bioremediation studies not indexed by Scopus might not have been included. Therefore, other well-known databases, such as WoS, should be used and incorporated with Scopus to obtain a vast amount of Bioremediation literature, which is expected to increase the reliability of the findings.

Future research directions should focus on addressing these structural gaps. Interdisciplinary integration connecting microbiology, soil chemistry, data science, environmental engineering, climate modeling, and policy studies are essential for advancing holistic remediation strategies. Moreover, emerging contaminants such as pharmaceuticals, nanoplastics, and heavy metal microplastic interactions require urgent attention. The adoption of machine learning, genome editing tools, synthetic biology, and multi-omics approaches can significantly accelerate the discovery of robust microbial strains and optimize remediation efficiency under variable environmental conditions. Finally, bioremediation research should expand beyond laboratory-scale experiments toward large-scale field applications, socio-environmental evaluations, and sustainable transition pathways.