Current State-of-the-Art of NGS in Soil Microbial Ecology Interpreted Through the Hierarchical Environmental Filtering (HEF) Framework

Next-generation sequencing (NGS) has transformed soil microbial ecology by revealing taxonomic and functional diversity that was largely inaccessible through cultivation-based approaches. However, greater sequencing resolution alone does not explain why particular microbial assemblages repeatedly emerge under specific soil and environmental conditions. This structured narrative conceptual review examines the current state of NGS-based soil microbiome characterization and introduces Hierarchical Environmental Filtering (HEF) as a framework for interpreting microbial community assembly. We discuss advances from amplicon sequencing to shotgun metagenomics, long-read sequencing, multi-omics, and computational analysis, together with limitations related to sampling, DNA extraction, primer selection, sequencing depth, bioinformatics, reference databases, and relic DNA. Within HEF, pedogenesis establishes a historically contingent physicochemical template, whereas contemporary climate, vegetation, rhizosphere processes, biotic interactions, dispersal, and stochastic processes modify assembly within that template. Anthropogenic disturbances can alter several levels simultaneously and may partially override inherited soil constraints. Soil microbiomes should therefore be interpreted as dynamic outcomes of environmental selection across spatial and temporal scales. Integrating standardized NGS workflows with functional multi-omics and predictive computation should advance soil microbiome research from descriptive inventories toward a mechanistic understanding of community assembly.