Resident soil microbial diversity and urea amendment legacy interact to shape the composition and expression of a surface film-forming soil inoculant

Abstract

Soil microbial inoculants have the potential to improve crop yield, enhance agricultural sustainability, and support soil restoration, but they often display unpredictable in-field performance across varied soil conditions. Cyanobacteria-dominated soil surface consortia (SSCs) offer a tractable model for studying inoculant-soil interactions because their visible surface growth enables direct observation and sampling after application. Here, we introduced the SSC "DG1," dominated by the diazotrophic cyanobacterium Nostoc linckia, into soil microcosms differing in resident microbiome diversity (low vs. high diversity) and urea fertilization history, (+urea vs. -urea). We used 16S rRNA gene sequencing and genome-resolved metatranscriptomics to assess inoculant establishment and functioning. Resident microbiome diversity did not affect total N. linckia gene expression, but heterotrophic DG1 members showed reduced expression in high-diversity soils. Soil diversity and urea history drove broad shifts in DG1 transcription and significantly affected transcription of key N. linckia carbon and nitrogen metabolism genes. High-diversity soils with urea were associated with increased transcription of photosynthesis, CAZyme, and nitrogen cycling genes, whereas low-diversity soils without urea promoted increased nitrogenase transcription and reduced carbon and nitrogen metabolism transcription. These results show that inoculant outcomes depend not only on establishment, but also how soil conditions and biology shape post-establishment functioning.