Profiling Active Low-Abundance Microbes in As/Sb-Contaminated Soils via d-Amino Acid-Based In Situ Labeling.

Area of Science:

• Environmental microbiology
• Geomicrobiology
• Metagenomics

Background:

• Soil microbes are crucial in contaminated environments.
• Distinguishing active microbes from potential function holders is challenging with traditional methods.

Purpose of the Study:

• To develop and apply a novel method for profiling active microbial communities in complex soils.
• To investigate the impact of metalloid contamination (As(V) and Sb(V)) on active microbial assemblages.

Main Methods:

• Utilized fluorescent d-amino acid labeling (FDAA) combined with fluorescence-activated cell sorting (FACS) and metagenomics (FDAA-FACS-Metagenomics).
• Applied secondary addition of As(V) and Sb(V) to assess microbial response.
• Recovered and analyzed Metagenome-Assembled Genomes (MAGs) of active microbes.

Main Results:

• FDAA-FACS-Metagenomics successfully captured and profiled active microbes, revealing community shifts under metalloid stress.
• Clostridium and other low-abundance taxa were activated as key reducers of As(V)/Sb(V).
• Identified functional partitioning within the active community, with some taxa directly involved in reduction and others providing stability.

Conclusions:

• Rare, metabolically active microbes play significant roles in metalloid transformation and soil ecosystem functioning.
• A specific Desulfitobacteriaceae genome (MAG29) exhibits metabolic versatility, including metalloid reduction, carbon fixation, and nitrogen fixation.
• This metabolic potential suggests MAG29's contribution to coupled biogeochemical cycles under contaminated conditions.