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Team IDs Fungi on Coffee Leaves in Search of Coffee Rust Control Candidates

NEW YORK (GenomeWeb) – A sequencing-based analysis of fungal species on coffee plant leaves from farms in southern Mexico and central Puerto Rico has uncovered organisms that might eventually prove useful for thwarting another fungus: the coffee rust-causing pathogen Hemileia vastatrix.

"Latin America is experiencing unprecedented epidemics of coffee rust, so identification of its natural enemies could aid in developing management strategies or in pinpointing species that could be used for biocontrol," University of Michigan ecology and evolutionary biology researcher Timothy James, the study's corresponding author, said in a statement.

James and his colleagues used Pacific Biosciences' single-molecule real-time sequencing platform to detect DNA from hundreds of fungal species in dozens of coffee leaf samples. Their findings, published online today in Applied and Environmental Microbiology, suggest even small coffee leaf samples can harbor dozens of fungal taxa.

"We recovered a surprisingly high fungal diversity in extraordinarily small samples of coffee leaf material," James explained. "These hyper-diverse communities highlight the complexity of fungal diversity of unknown ecological function within these leaves."

Moreover, he and his co-authors noted, the identification of 15 species known to be parasites of other fungi pointed to the possibility of mining the data for organisms that could control coffee rust.

The coffee rust-causing fungus H. vastatrix is currently taking a toll on Latin American coffee plantations, the team pointed out, leading to declines in productivity coupled with increased spending on control efforts.

In a search for naturally occurring organisms that might offset the negative effects of H. vastatrix, the researchers collected 46 hole punch-sized coffee leaf samples with or without coffee rust lesions from three farms in the Soconusco region of Chiapas in Mexico and from five farms located in the Central Mountain region of Puerto Rico.

To characterize fungal communities in a culture-free manner, the team used primers targeting fungal ribosomal RNA internal transcribed spacer regions to generate amplicons for subsequent sequencing analyses.

These amplicons were produced under experimental conditions designed to deter amplification of H. vastatrix sequences, the researchers explained, so that the fungal community analysis would not be swamped out by coffee rust sequences.

Instead, PCR experiments targeting H. vastatrix sequences were used to verify the presence or absence of the pathogen in leaf lesion samples and lesion-free control samples.

After selecting two dozen samples for further characterization, collaborators at the University of Michigan sequencing core sequenced the ITS amplicons with the PacBio RS II instrument, generating reads that corresponded to fungi from 313 operational taxa units.

The tally stretched to nearly 800 OTUs when the team considered organisms represented only once in the collection.

The diverse group included 15 potential mycoparasite species suspected of preying on other fungi, though the study's authors suspect still more mycoparasites could turn up with more refined molecular markers.

"[T]he mycoparasitic 'species' identified here are likely an underestimate because of the lack of resolution provided by the ITS rRNA marker locus that we used," they wrote.

Each sample carried fungi from between 13 and 69 OTUs, the team noted. And it saw more pronounced differences in the fungal communities from Puerto Rico and Mexico than from leaves with or without coffee rust disease.

Even so, coffee rust-affected leaves at farms from both countries contained high levels of an OTU that appeared to represent Colletotrichum gloeosporioides, a species believed to thwart some fungal infections in cacao plants.

"Ultimately," the researchers explained, "culturing these putative mycoparasitic fungi will be needed to better understand their effects on H. vastatrix and coffee."