Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

Authors: HANSEN, FREDRICK - New Mexico State University; James, Darren; ANDERSON, JOHN - New Mexico State University; MEREDITH, CHRISTY - Montana Department Of Environmental Quality; DOMINGUEZ, ANDREW - New Mexico State University; POMBUBPA, NUTTAPON - University Of California, Riverside; STAJICH, JASON - University Of California, Riverside; ROMERO-OLIVARES, ADRIANA - New Mexico State University; SALLEY, SHAWN - Natural Resources Conservation Service (NRCS, USDA); PIETRASIAK, NICOLE - New Mexico State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2023
Publication Date: 6/7/2023
Citation: Hansen, F.A., James, D.K., Anderson, J., Meredith, C., Dominguez, A.J., Pombubpa, N., Stajich, J.E., Romero-Olivares, A.L., Salley, S.W., Pietrasiak, N. 2023. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert. Frontiers in Microbiology. 14. Article 1135800. https://doi.org/10.3389/fmicb.2023.1135800.
DOI: https://doi.org/10.3389/fmicb.2023.1135800

Interpretive Summary: This study examined soil microbial diversity in four microbial groups (total bacteria, cyanobacteria, archaea, and fungi) from soil samples collected at 15 locations in the Jornada Basin. It found that landscape features including parent material, vegetation type, landform type, and ecological sites and states have a stronger influence on microbial community composition than on microbial species diversity, especially for fungi. Although more research is needed, these findings can help inform the understanding of ecological processes in drylands.

Technical Abstract: Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total bacteria, cyanobacteria, archaea, and fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, electrical conductivity. Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. With the exception of richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha and beta diversity indices (p = 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on microbial community composition than on alpha diversity, especially for fungi. Soil texture, pH, salinity, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.