A conceptual framework for the phylogenetically constrained assembly of microbial communities

Area of Science:

• Ecology
• Microbiology
• Evolutionary Biology

Background:

• Microbial communities are crucial for ecosystem function, impacting human health and agriculture.
• Understanding microbial community assembly is key to managing these ecosystems effectively.
• Deterministic processes significantly influence microbial community assembly, evidenced by phylogenetic signals and conserved traits.

Discussion:

• A novel framework for microbial community assembly is proposed, based on phylogenetically constrained principles.
• This framework predicts the existence of phylogenetic core groups (PCGs) occupying specific niches.
• PCGs are defined as conserved phylogenetic clusters essential across ecosystem instances, possessing specific, conserved traits.

Key Insights:

• The framework integrates ecosystem patchiness, microbial interactions, and sampling scales for a comprehensive model.
• Phylogenetic core groups (PCGs) are identifiable using high-throughput 16S amplicon sequencing.
• Analysis of PCGs' phylogeny, core pan-genome, and co-occurrence reveals ecophysiology and niche characteristics.

Outlook:

• This approach offers a priori information to enhance complementary analyses of microbial communities.
• The proposed framework represents a significant advancement in understanding microbial community assembly and function.
• Further research can leverage PCG identification to predict and manipulate microbial community behavior.