Little is known about the community dynamics of fungi on decomposing fine roots, despite the importance of fine roots as a source of carbon to detrital systems in forests. We examined fungal communities on dead roots in a sugar-maple dominated northern hardwood forest to test the hypothesis that community development is sensitive to rhizosphere disruption. We generated cohorts of dead fine roots in root windows and disturbed the rhizosphere microbial community in half of the windows by moving roots into sieved bulk soil. We sampled root fragments repeatedly over time and cultured fungi from these fragments to explore temporal patterns of fungal species composition. Disturbing the root rhizosphere prior to initiating decomposition changed the dominant fungal taxa, the distribution of dominant species within the community, and the temporal development in the culturable fungal community. Dominance in control roots shifted from Neonectria in early decay to Umbelopsis in later decay. Disturbance roots were more evenly dominated over time by Trichoderma, Neonectria, another species of Umbelopsis, and Pochonia. Our results suggest that species interactions are important in the ecology of fine root decay fungi, with the rhizosphere community of the living root influencing development of the decay community.
Whole Genome Sequence (WGS) based identifications are being increasingly used by regulatory and public health agencies to facilitate the detection, investigation, and control of pathogens and pests. Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant vascular wilt pathogen of cultivated cotton, and consists of several pathogenic races that are not each other’s closest phylogenetic relatives. We have developed WGS assemblies for isolates of race 1 (FOV1), race 4 (FOV4), race 5 (FOV5), and race 8 (FOV8) using a combination of Nanopore (MinION) and Illumina sequencing technology (Mi-Seq). This resulted in assembled contigs with more than 100X coverage for each of the FOV races and estimated genome sizes of FOV1 52 Mb, FOV4 68 Mb, FOV5 68 Mb and FOV8 55 Mb. The AUGUSTUS gene prediction program predicted 16,263 genes in FOV1, 20,259 genes in FOV4, 20,375 genes in FOV5 and 16,615 genes in FOV8. We were able to identify 525 genes unique to FOV1, 570 unique to FOV4, 1242 unique to FOV5 and 383 unique to FOV8. We expect that these findings will help in comparative genomics, and in the identification of unique genes as candidate targets for diagnostic marker and methods development to permit rapid differentiation of FOV subgroups.
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