Eight years of manure fertilization favor copiotrophic traits in paddy soil microbiomes

The application of organic matter to agricultural land is an efficient way to maintain soil eco-sustainability through the mediation of the soil-dwelling microbiome. Despite their important role in soil health, trait-based changes within cross-kingdom microbial communities following organic fertilization in soils are still poorly characterized. Here, shotgun metagenomic sequencing was used to examine microbial taxonomic and functional composition when subjected to a fertilization gradient, in which increasing amounts of cow manure have been continuously applied to paddy lands over 8 years. Organic fertilization did not have significant effects on the richness and diversity of soil microbial communities (bacteria, archaea, or fungi), nor the overall archaeal or fungal community compositions. However, bacterial communities were highly responsive to the fertilization gradient, and a unidirectional and progressive shift was observed. Notably, over 95% of bacterial taxa showing significant changes in relative abundances could be classified as copiotrophic taxa, such as those assigned to the Proteobacteria and Actinobacteria; in contrast, those in non-fertilized soils were mostly assigned to Acidobacteria, which is an oligotrophic group. Coupled with these changes, indices such as the decreased ratios of unclassified bacterial taxa to the total taxa with fertilization provided both direct and indirect lines of evidence for shifts towards a higher proportion of microbes with a copiotrophic lifestyle in fertilized soils compared with controls. Besides, the relative abundances of functional genes responsible for nutrient cycles (e.g., nitrate and sulfur reduction) as well as the degradation of complex organic compounds (e.g., lignin) were generally enriched with fertilization compared with the controls, implying a potential for preferentially enhanced nutrient biogeochemical processes with the higher proportion of copiotrophic microbes in fertilized soils. The present work helps to identify trait-based shifts in cross-kingdom soil microbial communities under organic fertilization, for the better evaluation of sustainable eco-agricultural management from a microbial community viewpoint.

Automated summary

The application of organic matter to agricultural land can maintain soil eco-sustainability by mediating the soil-dwelling microbiome. This study using shotgun metagenomic sequencing found that organic fertilization did not significantly affect the richness and diversity of soil microbial communities, but bacterial communities were highly responsive to the fertilization gradient, showing a unidirectional and progressive shift.