Substrate uptake patterns shape niche separation in marine prokaryotic microbiome

Area of Science:

• Marine microbiology
• Biogeochemical cycles
• Molecular ecology

Background:

• Marine heterotrophic prokaryotes are crucial for recycling organic matter in the ocean.
• Substrate uptake by prokaryotes is mediated by specific transporter proteins.
• Understanding transporter diversity is key to deciphering microbial roles in marine ecosystems.

Purpose of the Study:

• To investigate the size-fractionated patterns of prokaryotic transporter expression in the oceanic water column.
• To identify the taxonomic basis for variations in transporter expression.
• To elucidate the role of different transporter types in substrate assimilation and microbial lifestyles.

Main Methods:

• Multi-'omics' approach targeting ATP-binding cassette (ABC) transporters and TonB-dependent transporters (TBDTs).
• Analysis of transporter substrate specificity across different microbial taxa.
• Correlation of transporter expression patterns with microbial lifestyles and ecological roles.

Main Results:

• A size-fractionated pattern in prokaryotic transporter expression was observed, linked to taxonomic variations.
• Free-living microbes (SAR11, Rhodobacterales, Oceanospirillales) primarily use ABC transporters for organic nitrogen.
• Particle-associated microbes (Alteromonadales, Bacteroidetes, Sphingomonadales) utilize TBDTs for carbon-rich matter and metal chelates.
• Transporter expression supports distinct lifestyles, particularly in deep-sea prokaryotes.

Conclusions:

• Transporter divergency in organic matter assimilation signifies pronounced niche separation in marine prokaryotes.
• Microbial community structure and substrate availability drive transporter expression patterns.
• This study enhances our understanding of prokaryote-mediated organic matter cycling in marine environments.