Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

Abstract

Introduction: 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.

Methods: 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, and electrical conductivity.

Results: 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. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (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 relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations.

Discussion: 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.

Keywords: archaea; bacteria; biocrust; cyanobacteria (blue-green algae); dryland; fungi; soil geomorphic template; topsoil.

Figure 1

Location of the Jornada Basin in southern New Mexico, United States (top), the four major landscape components with 15 sites included in the study (center), and aerial imagery from representative sites for each vegetation zone studied including visible trampled walking paths (bottom). Site labels reflect vegetation zone components including creosote: C-CALI, C-GRAV, and C-SAND, grassland: G-BASN, G-IBPE, and G-SUMM, mesquite: M-NORT, M-RABB, and M-WELL, playa and bottomland: P-COLL, P-SMAL, and P-TOBO, and tarbush: T-EAST, T-TAYL, and T-WEST. Boundaries shown within the Jornada Basin are the Chihuahuan Desert Rangeland Research Center (lower left) and USDA-ARS Jornada Experimental Range (center and upper right). Aerial imagery was modified after Wojcikiewicz and Hanan (2022).

Figure 2

Taxonomic compositions of domain Bacteria, bacteria phylum Cyanobacteria (photoautotrophic only), domain Archaea, and phylum Fungi within domain Eukarya at the 15 long term NPP plots, Jornada Basin, New Mexico, United States. Plots show data from undisturbed samples. Numeric values of relative abundances appear in Supplementary Table 3.

Figure 3

Model-based means and standard errors of relative abundances for taxa in Bacteria, Archaea, Cyanobacteria, and Fungi with significant differences. Within a panel, means with the same letter are not different at α = 0.05.

Figure 4

Model-based means and standard errors of observed species richness. Within a panel, means with the same letter are not different at α = 0.05.

Figure 5

NMDS ordinations of Total Bacteria, Cyanobacteria, Archaea, and Fungi with overlaid environmental fit results of soil properties, lichen biocrust cover, and perennial plant biomass data. Only significant environmental variables (p < 0.10) are shown as vectors.