Investigating the core microbiome concept: Daphnia as a case study.

Area of Science:

• Microbiology
• Ecology
• Freshwater Biology

Background:

• Host-associated microbiomes are crucial for organism fitness and ecosystem function.
• The cladoceran Daphnia is a key freshwater grazer, making its microbiome vital for ecosystem stability.
• Understanding the Daphnia microbiome is essential for interpreting host-microbiota interactions and ecosystem dynamics.

Purpose of the Study:

• To identify the core microbiome of Daphnia magna, focusing on consistently present microbial taxa.
• To determine if a stable, core microbiome exists across different Daphnia populations and environments.
• To assess the influence of laboratory versus field conditions on Daphnia microbiome composition.

Main Methods:

• Compiled a dataset from 12 published studies on Daphnia magna microbiomes.
• Analyzed gut and whole-body samples from laboratory-cultured and field-grown Daphnia.
• Employed quantification metrics based on prevalence and relative abundance to identify core taxa.

Main Results:

• The Daphnia magna microbiome exhibits high variability across studies and conditions.
• Limnohabitans planktonicus showed consistent association, particularly in laboratory-cultured Daphnia.
• Field-grown Daphnia displayed more diverse microbiomes with a reduced presence of L. planktonicus, challenging its core status.

Conclusions:

• The Daphnia magna microbiome is characterized by variability and limited conserved associations.
• L. planktonicus is a stable taxon in laboratory settings but not a core member in natural environments.
• Laboratory findings on Daphnia microbiomes require cautious interpretation for natural populations; further field research is needed.