Legacy effects of cropping system and precipitation influence core Camelina sativa microbiome

Authors: BARNES, ELLE - Lawrence Berkeley National Laboratory; Yin, Chuntao; Schlatter, Daniel; Peng, Hao; Willmore, Cody; LU, CHAOFU - Montana State University; TRINGE, SUSANNAH - Lawrence Berkeley National Laboratory; Paulitz, Timothy

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2024
Publication Date: 12/21/2024
Citation: Barnes, E., Yin, C., Schlatter, D.C., Peng, H., Willmore, C.G., Lu, C., Tringe, S., Paulitz, T.C. 2024. Legacy effects of cropping system and precipitation influence core Camelina sativa microbiome. Phytobiomes Journal. e-ISSN: 2471-2906. https://doi.org/10.1094/PBIOMES-08-24-0080-R.
DOI: https://doi.org/10.1094/PBIOMES-08-24-0080-R

Interpretive Summary: Camelina is a potential biofuels crop, in the Brassicaceae family. It is well adapted for dryland crop rotation. Nothing is known about the microbial communities on the roots, and the role they may play in the health of the plants. Soils were sampled from 33 locations across Eastern Washington, and camelina plants were grown in the soil in the greenhouse. DNA was isolated from the soil and roots, and the fungal and bacterial communities were characterized with amplicon sequencing. A core microbiome was described on the roots, despite the fact that the location, cropping system zone and rotations also had minor efffects on the community. In the zone around the roots, the Actinobacteria Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus were plant-selected, while inside the root was characterized by a number of Actinobacteria, Rhizobium and Clostridium. Sphingomonas ASVs were overrepresented in the zone around the root (high occupancy, lower abundance), which suggests that they are present in soils collected throughout eastern Washington regardless of soil origin.This study contributes to our understanding of the assembly of microbes in and around camelina roots while also highlighting the potential lasting impact cropping can have on soil and plant-associated microbial communities.

Technical Abstract: Camelina (Camelina sativa L.), a member of the Brassicaceae family, is a potential biofuel crop and has numerous rotation benefits in dryland cropping systems. However, little is known about the core root microbiome of camelina and the role of location, cropping systems zones, or crop rotation in driving the composition and diversity of camelina-associated microbiomes. Camelina was grown in soil collected from thirty-three locations in Eastern Washington in the greenhouse, and DNA was extracted from bulk soil, rhizosphere and endosphere. Bacterial, archaeal and fungal microbiomes were characterized with amplicon sequencing and a collection of over 3000 bacterial strains was isolated. Plants grown in soil from the annual cropping zone (highest precipitation) had higher alpha diversity in the bulk soil than those from the driest wheat-fallow zone, but this effect was not seen in the rhizosphere and endosphere. Plant compartment, cropping system zone, and location had significant effects on microbial beta diversity. Abundance-occupancy distributions were used to identify a core subset of microbes that associate with camelina roots regardless of soil legacy. In the rhizosphere, the Actinobacteria Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus were plant-selected, while the endosphere was characterized by a number of Actinobacteria, Rhizobium and Clostridium. Sphingomonas ASVs were overrepresented in the rhizosphere (high occupancy, lower abundance), which suggests that they are present in soils collected throughout eastern Washington regardless of soil origin. Fusarium and Mortierella were overrepresented in the endosphere. In contrast, fungi known to be lignin decomposers, such as Agrocybe, Coprinellus, and Macrocystidia, were underrepresented in the endosphere (high abundance, low occupancy) suggesting that these taxa may be dispersal-limited or location-specific rhizosphere colonists, perhaps due to the legacy effect of longstanding wheat cropping. This study contributes to our understanding of the assembly of microbes in and around camelina roots while also highlighting the potential lasting impact cropping can have on soil and plant-associated microbial communities.