Closing the gap between the number of Phytophthora species isolated through baiting a soil sample and the number revealed through metabarcoding

Abstract

This review assesses possible reasons for the discrepancy between the high numbers of Phytophthora species and putative new species isolated from environmental samples using metabarcoding, compared with the low number cultured and identified through bating. Molecular protocols are unlikely to result in high numbers of false positives, except that variants in young hybrid species may be incorrectly identified as different species. Baiting conditions favour parasitic species that are fast to sporulate, able to infect a range of bait species, achieve infection with a low number of zoospores, and fast-growing on selective agar. Species may not be isolated because they are slow-growing saprophytes and slow to sporulate when baited. Changes to protocols that might result in the isolation of more species include changes in the timing of exposure of baits, inclusions of dead baits, reducing potential competition from fast-growing species by baiting only small volumes of soil, and isolation on media without antimicrobials. However, the species not isolated may have growth traits precluding easy isolation, such as host specificity or obligate biotroph lifestyle.