Title of Research Project
The contribution of foliar fungi to agricultural soil microbiomes in an organic cropping system
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Major
Biology
Research Abstract
With finite arable land available to support a growing human population, sustainable agricultural techniques are essential for long-term food security. One sustainable cropping technique is cover cropping, when a non-cash crop is planted to replenish soil nutrients or improve soil structure. While these benefits are well known, one under-explored effect of cover cropping is its potential ability to reduce pathogen burden on cash crops. One mechanism by which this reduction in disease severity may occur is via endophyte-pathogen interactions. Endophytes are endosymbionts that live asymptomatically within plants and have been observed to alleviate disease symptoms within their host. Our objective is thus to determine the extent to which foliar microbiomes from cover crops (purple vetch, Vicia americana; daikon radish, Raphanus sativus var. longipinnatus; and fava beans, Vicia faba) contribute to soil and cash crop microbiomes in an organic agricultural setting. In coordination with a working farm in Marin County, California, we sampled cover crop leaves and soil cores prior to the start of the cash crop growing season. Leaves were surface sterilized and placed into slant tubes with malt extract agar to isolate emergent foliar fungi. Microbial slant tube growth was quantified, and fungal isolates were identified using Sanger sequencing. Slant tube fungal growth showed that cover crop type had a significant influence on fungal isolation frequency (n = 29, Kruskal-Wallis p < 0.05) with leaves of daikon radish having the highest isolation frequency. Using barcode sequencing of the Internal Transcribed Spacer (ITS) locus, the most common fungal genus found was Alternaria for daikon radish, Cladosporium for purple vetch, and Nemania for fava beans. Fava beans showed the highest diversity (Shannon diversity = 2.39), followed by daikon radish (2.21) and purple vetch (1.81). Out of 55 genera, only eleven were found in more than one cover crop. We will process these same samples for high-throughput Illumina sequencing to develop a higher-resolution description of these communities. We will also carry out greenhouse experiments to test pathogen mitigation effects of the most common culturable endophytes. Together, these results will offer new insight into an understudied aspect of organic cropping systems, with potential applied benefit to agriculture.
Faculty Mentor/Advisor
Naupaka Zimmerman
The contribution of foliar fungi to agricultural soil microbiomes in an organic cropping system
With finite arable land available to support a growing human population, sustainable agricultural techniques are essential for long-term food security. One sustainable cropping technique is cover cropping, when a non-cash crop is planted to replenish soil nutrients or improve soil structure. While these benefits are well known, one under-explored effect of cover cropping is its potential ability to reduce pathogen burden on cash crops. One mechanism by which this reduction in disease severity may occur is via endophyte-pathogen interactions. Endophytes are endosymbionts that live asymptomatically within plants and have been observed to alleviate disease symptoms within their host. Our objective is thus to determine the extent to which foliar microbiomes from cover crops (purple vetch, Vicia americana; daikon radish, Raphanus sativus var. longipinnatus; and fava beans, Vicia faba) contribute to soil and cash crop microbiomes in an organic agricultural setting. In coordination with a working farm in Marin County, California, we sampled cover crop leaves and soil cores prior to the start of the cash crop growing season. Leaves were surface sterilized and placed into slant tubes with malt extract agar to isolate emergent foliar fungi. Microbial slant tube growth was quantified, and fungal isolates were identified using Sanger sequencing. Slant tube fungal growth showed that cover crop type had a significant influence on fungal isolation frequency (n = 29, Kruskal-Wallis p < 0.05) with leaves of daikon radish having the highest isolation frequency. Using barcode sequencing of the Internal Transcribed Spacer (ITS) locus, the most common fungal genus found was Alternaria for daikon radish, Cladosporium for purple vetch, and Nemania for fava beans. Fava beans showed the highest diversity (Shannon diversity = 2.39), followed by daikon radish (2.21) and purple vetch (1.81). Out of 55 genera, only eleven were found in more than one cover crop. We will process these same samples for high-throughput Illumina sequencing to develop a higher-resolution description of these communities. We will also carry out greenhouse experiments to test pathogen mitigation effects of the most common culturable endophytes. Together, these results will offer new insight into an understudied aspect of organic cropping systems, with potential applied benefit to agriculture.
