The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern Washington
Authors:
Hao Peng1* (hao_peng@wsu.edu), Elle M Barnes2, Chuntao Yin3, Daniel Schlatter4, Cody Willmore5, Timothy Paulitz1,5, Susannah G Tringe2,6, and Chaofu Lu7
Institutions:
1Washington State University; 2DOE Joint Genome Institute; 3U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Brookings, SD; 4USDA-ARS, St. Paul, MN; 5USDA-ARS, Pullman, WA; 6Lawrence Berkeley National Laboratory; and 7Montana State University
Goals
Identify microbial diversity of the soil, rhizosphere, and root of the oilseed crop, Camelina sativa; Determine the effects of cropping zone and precipitation on microbial composition; Characterize the core bacterial and fungal microbiome of Camelina.
Abstract
Camelina sativa L. is a broadleaf member of the Brassicaceae family. A short season crop (85 to 100 days), Camelina is fairly disease- and pest resistant, drought- and frost tolerant, and can be grown under low-input conditions (Gao et al. 2018; Zanetti et al. 2017; Matteo et al. 2020; Neupane et al. 2022; Séguin-Swartz et al. 2009). An important part of the success of this plant under low-input conditions may be attributed to its rhizosphere and endosphere microbiome, but to date there have been no publications on the microbiome of Camelina. In this study, soil was collected from 33 sites across a 200 km gradient in the dryland wheat production area in eastern Washington. This included four main cropping zones based on precipitation: wheat/summer fallow (< 300 mm/yr), intermediate (300 to 450 mm/yr), annual cropping zone (450 to 600 mm/yr) and south (400 to 500 mm/yr). Camelina was planted into the soils in the greenhouse. After six weeks, plants were harvested and DNA was extracted from root, rhizosphere and bulk soil. Bacterial 16S rRNA and fungal internal transcribed spacer (ITS) amplicons were amplified and sequenced with Illumina MiSeq (Gohl et al. 2016). Researchers then identified the core Camelina microbiome using an abundance-occupancy model (Shade and Handelsman 2012; Shade and Stopnisek 2019). They found that microbiome diversity decreased from the soil to the endosphere and, for the soil microbiome, increased with average precipitation. Plant compartment, zone, previous crop, and site all significantly affected composition of the Camelina microbiome, with the largest differences seen between the annual cropping zone and wheat/summer fallow zone. Several Actinobacteriota and Alphaproteobacteria (e.g., Actinoplanes, Aeromicrobium, Mycobacterium, Rhizobium, Caulobacter, and Sphingomonas) and two fungi (e.g., Pseudogymnoascus and one unidentified ASV) were differentially abundant in the plant-associated core microbiome. Fitting the abundance-occupancy model to the Sloan neutral model of community assembly provided additional evidence that these genera appear to be deterministically selected by the plant, suggesting that these core genera may possess traits that would make them good candidates for efficient plant colonization.
References
Gao, L., et al. 2018. “Photosynthesis and Growth of Camelina and Canola in Response to Water Deficit and Applied Nitrogen,” Crop Science 58(1), 393–401.
Zanetti F., et al. 2017. “Agronomic Performance and Seed Quality Attributes of Camelina (Camelina sativa L. Crantz) in Multi-Environment Trials Across Europe and Canada,” Industrial Crops and Products 107, 602–08.
Matteo, R., et al. 2020. “Camelina (Camelina sativa L. Crantz) Under Low-Input Management Systems in Northern Italy: Yields, Chemical Characterization and Environmental Sustainability,” Italian Journal of Agronomy 15(2), 132–43.
Neupane, D., et al. 2022. “Realizing the Potential of Camelina sativa as a Bioenergy Crop for a Changing Global Climate,” Plants 6, 772.
Séguin-Swartz, G., et al. 2009. “Diseases of Camelina sativa (False Flax),” Canadian Journal of Plant Pathology 4, 375–86.
Gohl, D.M., et al. 2016. “An Optimized Protocol for High-Throughput Amplicon-Based Microbiome Profiling,” Nature Protocol Exchange. DOI:10.1038/protex.2016.030.
Shade, A. and Handelsman, J. 2012. “Beyond the Venn Diagram: The Hunt for a Core Microbiome,” Environmental Microbiology 1, 4–12.
Shade, A. and Stopnisek, N. 2019. “Abundance-Occupancy Distributions to Prioritize Plant Core Microbiome Membership,” Current Opinion in Microbiology 49, 50–58.
Funding Information
This research was supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research Program, Genomic Science Program grant no. DE-SC0021369, and Contract No. DE-AC02-05CH11231 to the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility.