DNA and RNA metabarcoding reveal shared dominant seed-borne fungi

Area of Science:

• Ecology
• Mycology
• Molecular Biology

Background:

• Tree seeds host diverse fungal communities, including pathogens and mutualists, impacting plant health.
• Distinguishing active from inactive fungi is vital for phytosanitary monitoring, as only active fungi interact with hosts.
• Traditional culturing captures living fungi but misses much diversity; DNA metabarcoding detects more but includes non-viable cells.

Purpose of the Study:

• To compare fungal communities in seeds of European trees using culturing, DNA metabarcoding, and RNA metabarcoding.
• To evaluate the effectiveness of RNA metabarcoding in identifying active fungal communities in tree seeds.
• To assess the complementary roles of different methods in characterizing seed-associated fungi.

Main Methods:

• Culturing of fungi from tree seeds.
• High-throughput DNA metabarcoding.
• High-throughput RNA metabarcoding.

Main Results:

• Host species identity significantly shaped dominant fungal communities in seeds.
• DNA and RNA metabarcoding largely agreed on abundant genera, but RNA datasets highlighted rare taxa.
• Cultured genera, presumed active, were consistently detected by both DNA and RNA methods.

Conclusions:

• Culturing, DNA, and RNA metabarcoding offer complementary insights into seed-associated fungal diversity.
• RNA metabarcoding shows potential for identifying active fungal members for monitoring.
• Combining methods provides the most thorough fungal assessment for environmental and phytosanitary purposes.