Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

Area of Science:

• Microbial Ecology
• Genomics
• Bioinformatics

Background:

• Microbial evolution is significantly influenced by horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs).
• The nanobiome, comprising microbial hosts and their associated replicators, is crucial for understanding gene flux but remains understudied.
• Existing methods often struggle to differentiate MGE dissemination from demographic shifts in microbial communities.

Purpose of the Study:

• To develop and apply a novel bioinformatic pipeline (xenoseq) for identifying MGE dissemination within evolving microbial consortia.
• To investigate the impact of MGEs on complex microbial community structure and function.
• To characterize previously unknown members of the nanobiome and their roles in microbial evolution.

Main Methods:

• Development of the xenoseq bioinformatic pipeline for cross-comparing metagenomic samples.
• Application of xenoseq to compost microbial communities undergoing periodic mixing.
• Comparative metagenomic analysis to identify MGEs and their hosts.

Main Results:

• Xenoseq successfully distinguishes MGE movement from community demographic changes.
• Discovery of a parasitic nanobacterium (Candidate Phylum Radiation) related to 'Candidatus Saccharibacterium'.
• Identification of a large plasmid in a 'Cellvibrio' lineage, associated with nitrogen fixation and increased ammonia production.

Conclusions:

• New experimental and bioinformatic strategies are essential for understanding the nanobiome's role in microbial evolution.
• The nanobiome, including parasitic elements and plasmids, significantly impacts microbial community dynamics.
• Xenoseq provides a powerful approach to dissecting gene flux and its evolutionary consequences in microbial ecosystems.