Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.

Microbial agents play a crucial role in improving soil quality, increasing soil fertility, enhancing crop yields, and reducing the incidence of diseases. The ecological benefits of these products contribute to environmental protection and to the promotion of sustainable agricultural development. Since the beginning of the 21st century, research in the academic community on the use of microbial agents for soil improvement has increased, yet a systematic summary of the progress in this field is lacking. In this paper, we review trends in microbial agent applications, focusing on their classification, mechanisms of action, and practical implementations. To achieve this, we conduct a bibliometric analysis based on the SCI-EXPANDED database of the Web of Science, using tools such as VOSviewer for visualization. We focus on microbial agents for soil improvement and analyze publication trends, research hotspots, and annual variations in relevant studies published between 2003 and 2024. The results show that (1) the number of publications on microbial soil improvement has steadily increased over the years, indicating that the academic community has maintained a high level of interest in this field. Keywords such as “soil”, “diversity”, “carbon”, and “nitrogen” have been central research hotspots in the past 20 years. The research has been highly concentrated in a few countries, including China and the United States, as well as in key institutions such as the Chinese Academy of Sciences and the United States Department of Agriculture. (2) We further analyze the principles governing microbial agent efficacy, address limitations in their application, and propose strategies to advance research in this field. Finally, several suggestions are proposed to promote the further development of research on microbial agents for soil improvement.