Spatiotemporal trends in spatial microbial ecology research publication and citation
Our search based on ‘topic’ showed a total 7627 publications between 2000 and 2020, and we retrieved 7022 documents after applying the exclusion and inclusion criteria, including 6450 (91.85%) articles and 572 (8.14%) reviews (Fig. 1). The temporal trend in the number of publications and the citation rate in the field of spatial microbial ecology from 2000 to 2020 (Fig. 2A) revealed a steady increase, with an accelerated rate after 2005 and a total of approximately 334.4 publications per year. We further divided the publication of documents into two temporal stages, from 2000 to 2010 and 2011 to 2020. The initial period showed low growth with an average 165 publications per year, while the later period showed an impressive trend of 520.8 publications per year. The 7022 retrieved documents received 252,980 citations, an average of 36.026 citations per item, with an h-index of 192. The temporal distribution of citations (Fig. 2B) indicated an average of 12,046.66667 citations per year. The spatial contribution of research in spatial ecology revealed that United States of America (USA) has dominated the contribution to this field with 2508 publications and 126,127 citations. Peoples Republic of China (PRC) ranked second with respect to publications, while Germany ranked second in term of citations. The worldwide publication and citation trends are shown in (Fig. S1).
Based on the authors' affiliations in the same publication as evidence of production and cooperation, an assessment of the contribution of various countries to the development of spatial microbial ecology studies was performed (Fig. S2). The nodes are the number of authors from the same region, and the interest of the country is the diameter of the node. The presence of an arc between the nodes indicates collaboration among researchers from different countries. The cluster reveals that scientific work occurred through established collaborations. In international cooperative partnerships in spatial microbial ecology research, the USA is perhaps the dominant country and holds a key role in the figure. The USA, China and Germany have played an important role in supportive collaboration among nations, with the majority of publications. The USA cooperated frequently with China, Germany, England, Japan and Canada. Among them, the US–China collaborative partnership was predominant and ranked first with 238 collaborative publications. China also cooperated effectively with other nations, such as Australia, England and Germany with 58, 52 and 44 publications, respectively.
Author productivity and collaboration in research
Author productivity is a valuable indicator of the most active researchers in a given field. A collaboration map illustrating the co-author network of the top 100 researchers is shown in (Fig. 3A). Each node represents an author, where the size of the node represents the number of documents authored by that author, the colour of the node represents the cluster to which the author belongs and the author-node relationship represents the author's co-authorship or research partnership. The cluster is a set of author-nodes that are closely connected. The wider the author-node, the greater the number of documents the author has written. The number of co-authored documents by the author-nodes on both sides of the link, as well as the research cooperation between those authors, rises as the link grows thicker. The fact that the author-nodes are the same colour suggests that they are closely related.
After excluding authors with fewer than five publications, there were 503 authors contributing 3657 publications on spatial microbial ecology. There are 80 authors in this field who have published more than ten articles. The top three most prolific authors in this field were Zhou, followed by Xie, Tedersoo, and Soininen, with 42, 27, 26 and 26 publications, respectively (Table S1). The co-citation analysis reveals that the work of Knight secured first position with 10,289 citations, followed by Fierer with 9382 total citations and Lauber with 7101 total citations in the second and third positions, respectively. Details of the top cited works are shown in (Fig. 3B). In addition, as shown in (Tab. S1), the average citation frequencies of these authors per publication were also in the top three, but in descending order: Lauber. (1420), Knight (489) and Fierer (426).
From 2000 to 2020, a total of 1178 journals published articles on spatial ecology, with 5599 articles published in a diverse range of 270 journals after excluding journals with fewer than five publications (Fig. S3a). The top ten most productive journals (TP >100) published a total of 1867 articles (33.34%). Frontiers in Microbiology, FEMS Microbiology Ecology and Plos One were the top three journals with the most publications (Table S2). In addition, we evaluated the citations received by these journals. (Fig. S3b). A list of the top ten journals with the highest numbers of citations is shown in (Table 1). Applied and Environmental Microbiology ranked first, indicating that it has a significant impact in this field. Similarly, Proceedings of the National Academy of Sciences of the United States of America and International Society of Microbial Ecology (ISME) ranked second and third, respectively, with over 9500 citations and high citation frequencies (Table 1).
Contributions of institutes
By analysing the distribution of the research institution where the author works, we can understand the scientific research capabilities and the research atmosphere of the institution. There were 397 different institutions worldwide showing research interest in spatial microbial ecology, so we set the threshold value for the total number of research institutions’ publications at 10. Only five of these institutions (0.89% of the total) published more than 100 papers. We selected the top 100 institutes for network analysis as shown in (Fig. S4a). From these 100 selected institutes, the ten most highly productive institutes are listed in (Table S3). Among these institutes, four of them were from the USA, two were from China and one was from each of Spain, France, Finland and Denmark. The Chinese Academy of Sciences had the most publications (498), greatly outnumbering any other institution. The second research institute was University of Chinese Academy of Sciences, which had 166 publications. The third most productive research institute was the National Institute for Agricultural Research, which had 125 published articles.
The US institutions continued to be the leaders in this field (Table S3). Furthermore, research universities accounted for six of the top ten most productive institutes, as well as seven of the top ten most citated institutes. This reflects the fact that research universities are at the forefront of this field. According to citation analysis, there were at least 2000 citations for 58 organizations, as shown in (Fig. S4b). The University of Colorado had the most citations (14,845), followed by the Chinese Academy of Science and Stanford University, each of which had 8958 and 8791 citations.
Co-citation analysis on cited authors
The most often cited authors and relevant information may be retrieved from the author co-citation network based on the number of co-citation occurrences. The weight of the author's citations is reflected by the size of each node. The links reflect a cooperative relationship between two authors. This study used co-citation analysis to create a map of 1000 authors that consisted of five clusters, as shown in (Fig 4A). The top three positions in terms of total co-citation frequencies were secured by Fierer (1176), Edgar (1161) and Caporaso (1140 citations). Furthermore, author burst detection can determine which author has had the greatest influence over a given period. The top 24 authors’ bursts are shown in (Fig. 4B). In the authors’ citation burst detection analysis, the strongest burst belonged to author Xie with a strength of 6.91, followed by Deng and Noah. There was a burst of nine authors that lasted until 2020.
Co-citation analysis of cited references
The analysis of references is an important aspect of bibliometrics-based visualization, as it reflects the field’s research database. In addition, it is also an important source for exploring the research context and direction of development . We used CiteSpace to draw the cited reference map based on the co-citation network and to analyse the cited references in the field of spatial microbial ecology. The pruning algorithm consisted of the Pathfinder, pruning sliced networks and pruning the merged network. We were able to obtain the visual network after running Citespace. The key co-citation clusters on the network were labelled by titles, as shown in (Fig. 5). In this network, there were 1614 nodes and 3146 edges. The network density was 0.0059. The Modularity Q was 0 .8017 (Q > 0.3), which generally indicates a significant clustering structure, and the Mean Silhouette was 0.898, which were important criteria for evaluating the validity of the mapping. The Q and S values (Fig. 5) indicate that the clustering structure was significant and that the clustering result was reasonable. The network was divided into 17 clusters of co-citation networks, which were then labelled on their own citers by index terms. The top six clusters are summarized (Table 2). Briefly, the largest cluster (#0) is a biogeographic pattern with 227 members and a silhouette value of 0.876. The most active citer in this cluster is Jiao (2020). The second largest cluster (#1), categorized as fungal communities, has 201 members and a silhouette value of 0.869, with the majority of the references published in 2012. Griffiths (2011) is the most active citer in this cluster. The third largest cluster, named ectomycorrhizal fungi, has 194 members, and the active citer is Hang-wei (2013). It is worth noting that the highest ranked item by citation, burst and centrality belongs to cluster #3.
The timeline visualization of the references co-citation analysis network is shown in (Fig. S5). Timeline visualization analysis showed that clusters #3, #8 and #13 are labelled as bacterial 16s, Picea abies and anaerobic process evaluation, respectively, indicating the beginning of work in this era. However, the longest clusters depicted in the timeline visualization is cluster #8, labelled as Picea abies. Besides this, clusters #0, cluster #1 and cluster #7, labelled as biogeographic pattern, fungal communities and spatial organization, respectively, are the most popular now, and they have been going on for many years.
In addition, citation bursts have been successfully applied to capture the sharp increase in a relevant research interest. The top 30 burst references generated by CiteSpace are shown in (Fig. S6). In the figure the dark blue line represents the time after publication, while the red line represents the beginning and ending time of the literature as a research hotspot. It also demonstrates that only five references had the strongest citation bursts before 2010, with Microbial biogeography: putting microorganisms on the map, published by Martiny coming first with a strength of 41.3 . During this time, they were primarily concerned with microbial distribution. Following 2010, many of the references had the strongest citation bursts, in which QIIME, published by Caporaso with a strength of 53.12, allowed analysis of high-performance community sequence data . The most recent reference with citation bursts appeared in 2018, and six references had a burst that lasted until 2020.
Co-citation analysis of keywords
The keywords are generalizations of the topics in the literature . We performed an analysis of keywords that can be used to determine the hotspots in the field of spatial microbial ecology. It is also used to track hot topics and research trends . A total of 808 keywords were found, eight of which have a frequency greater than 500. It shows the network of co-occurring terms, which includes 808 nodes and 4698 links. The node in the network represented a keyword, and its size depended on the frequency of co-occurrence. The keywords with high frequencies included diversity (2146), bacteria (747) and microbial community (662) (Fig. 6A).
Keyword burst detection also showed that many burst keywords emerged in 2000–2010 (Fig. 6B). The burst strength of 16s ribosomal RNA was 29.45, and the burst in 16s ribosomal RNA research in 2000 lasted until 2011, suggesting that 16s ribosomal RNA is a hotspot in spatial microbial studies. This also corresponds to the keyword diversity, because studies on diversity rely on 16s ribosomal RNA data. Prior to 2010, researchers used basic biological techniques to study microbial ecology, including keywords like ‘in situ hybridization’, ‘PCR’, ‘DGGE’, ‘T-RFLP’, ‘gradient gel electrophoresis’, ‘biome’, ‘spatial heterogeneity’, ‘community structure’, ‘geostatistics’, ‘gene’ and ‘assemblage’. After 2010, the application of some advanced methods and technologies, such as the keywords ‘pyrosequencing’, ‘high-throughput sequencing’ and ‘database’, has further advanced the research in this field.