Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome

Area of Science:

• Marine microbiology
• Sponge holobiont research
• Culturomics

Background:

• Sponges harbor diverse microbial communities crucial for ecological and biotechnological applications.
• Current cultivation methods struggle to isolate the majority of sponge-associated bacteria.

Purpose of the Study:

• To identify cultivation bottlenecks for sponge bacteria.
• To assess the impact of sample processing and cultivation conditions on bacterial recovery.
• To understand the relationship between viable and cultivable bacterial communities in sponges.

Main Methods:

• Combined high-throughput 16S rRNA gene sequencing with diverse cultivation media and incubation conditions.
• Isolated 325 sponge bacteria from Cymbastela concentrica and Scopalina sp.
• Used propidium monoazide (PMA) selective DNA modification to determine bacterial viability.

Main Results:

• Cultivable bacterial communities were host-specific, with distinct isolates obtained from different media.
• Approximately 97% of isolates were detected in the original sponge, representing a variable proportion of viable bacteria.
• Cultivation success primarily reflected the abundance of viable bacteria, not the total microbial community.

Conclusions:

• Bacterial cell viability and sample processing methods are critical factors limiting sponge bacterial cultivation.
• Cultivation yields are influenced by the viability of bacteria in the inoculum.
• Further research is needed to optimize sample processing for accurate representation of in situ sponge microbial communities.