European Journal of Sustainable Agroecosystems

Context: Understanding how soil microorganisms come together is a key issue in microbial ecology which has important implications for ecosystem recovery, farming efficiency, and global biogeochemical processes. Research based on amplicon sequencing such as 16S rRNA and ITS sequencing has allowed for better understanding of the taxonomic structure of communities but has drawbacks due to primer biases and low resolution as well as lacking the capability to analyze characteristics of soils. Use of shotgun metagenomics has changed the situation dramatically and provided researchers with an opportunity to address questions concerning ecological assembly in terms of ecological theory - more specifically, the dichotomy between deterministic selection and stochastic neutral processes.

Purpose of the review: The main purpose of this review is to provide an overview of structural, functional, and methodological findings obtained through metagenomic research conducted in 2015-2025.

Literature sources: For this purpose, a systematic literature search was performed in Scopus, Web of Science, PubMed, ScienceDirect, and SpringerLink.

Methodology of Review: Following the PRISMA guidance, a strict set-up narrowed 1,248 primary records down to the 34 keys, outstanding, works with peer-reviewing. They went under scrupulous scrutiny in terms of the method of research, sequencing methods, as well as ecological conclusions gained during the research.

The Main Outcomes: The synthesis carried out revealed that while deterministic selection is the key factor behind assembly of functional community (this being attributed to such factors as pH rate, \(\frac{C}{N}\) ratio, temperature,), it is stochastic processes (dispersal limitation and ecological drift) that are regarded as the dominating factors when it comes to taxonomic assembly. Shotgun metagenomics shows that functional redundancy conceals taxonomy changes, meaning different taxonomies can produce the same functionality under uniform environmental filters.

Significant Knowledge Gaps: One of the main gaps observed in the literature is heavy reliance on short-read sequencing (Illumina) which fails considerably in assembly of soils having complicated structure and therefore does not reflect the information on the dynamics of rare biosphere. Moreover, there seems to be a clear geographic bias in public reactions since more than 75% of the publications concentrate on temperate agricultural and North American or East Asian ecosystems, while tropical, arid