Genotype and Soil Management Practices Alter Abundance and Diversity of Culturable Carrot Endophytes.

Carrot is one of the most important vegetable crops in the world. Carrot roots are colonized by a wide variety of microorganisms (endophytes), but knowledge of how these communities are assembled or how they interact with plants to affect plant fitness are not well understood. Plant genotype and soil management practices are two factors likely to affect endophyte structure in carrot roots. In this study, nine carrot genotypes from wide genetic backgrounds were grown in conventional and organically managed crop systems. The roots were collected to quantify endophyte community structure. Culturalable fungal and bacterial endophytes were isolated using semi-selective media and identified using low throughput sequencing. Interestingly, Carrots grown in the organic system had higher endophyte diversity and abundance than those grown in the conventional system. Stenotrophomonas maltophilia, uncultured Xanthomonas spp., Xanthomonas Oryzae and Clamidosporum cladosporioides endophytes were identified in carrot roots grown in both systems. Additionally, endophytes abundance also varied among genotypes and there was a significant genotype X crop systems interaction with some genotypes. Exp 0191(Asia) genotype had dramatically more endophytes when grown in the organic system, whereas Exp 3999 (Brazil/Europe) genotype had relatively high endophyte density regardless of the production system. These results warrant further investigation as they may have important implications for plant fitness. For example, endophytes have been shown to suppress pathogen infection. In field trials, Exp 0191 (Asia) and Brasilia (Brazil) had greater foliar pathogen infection when grown in the conventional relative to the organic system. On-going experiments will better characterize endophyte community structure using culture independent techniques, and determine how such differences affect pathogen susceptibility in controlled studies.