Archaeal and Bacterial Diversity and Distribution Patterns in Mediterranean-Climate Vernal Pools of Mexico and the Western USA

Abstract

Biogeographic patterns in microorganisms are poorly understood, despite the importance of microbial communities for a range of ecosystem processes. Our knowledge of microbial ecology and biogeography is particularly deficient in rare and threatened ecosystems. We tested for three ecological patterns in microbial community composition within ephemeral wetlands-vernal pools-located across Baja California (Mexico) and California (USA): (1) habitat filtering; (2) a latitudinal diversity gradient; and (3) distance decay in community composition. Paired water and soil samples were collected along a latitudinal transect of vernal pools, and bacterial and archaeal communities were characterized using 16S rDNA sequencing. We identified two main microbial communities, with one community present in the soil matrix that included archaeal and bacterial soil taxa, and another community present in the overlying water that was dominated by common freshwater bacterial taxa. Aquatic microbial communities were more diverse in the north, and displayed a significant but inverted latitudinal diversity pattern. Aquatic communities also exhibited a significant distance-decay pattern, with geographic proximity, and precipitation explaining part of the community variation. Collectively these results indicate greater sensitivity to spatial and environmental variation in vernal pool aquatic microbial communities than in soil microbial communities. We conclude that vernal pool aquatic microbial communities can display distribution patterns similar to those exhibited by larger organisms, but differ in some key aspects, such as the latitudinal gradient in diversity.

Keywords: Archaea; Bacteria; Distance-decay; Environmental filtering; Ephemeral wetlands; Inverse latitudinal gradient.

Fig. 1

a North America Mediterranean-climate vernal pools. b Vernal pools extend along the Pacific West Coast in valleys and coastal mesas in California and Baja California. Climatic and geological features result in the formation of the vernal pools, which present c an aquatic phase characterized by flooding and soil saturation and d a terrestrial phase characterized by water evaporation and subsequent desiccation

Fig. 2

Microbial community analysis. a Beta Diversity: NMDS ordination analysis based on Bray–Curtis similarity coefficients. Soils and water have distinct microbial communities. b Alpha diversity by four different measures and by sample type. Soils (dry and wet) showed higher diversity in comparison with the water column: soil–water H = 18.9, P = 0.000013; wet soil–water H = 22.5, P = 0.000002; soil-wet soil H = 0.13, P = 0.71

Fig. 3

Taxonomic composition in water and soil samples, illustrating greater differences between water and soils than between wet and dry soils. a The relative abundance at phylum level across sample types; b Proteobacteria abundances across sample types; and c Bacteroidetes abundances across sample types

Fig. 4

Taxa abundance of Archaea at phylum level between soil, wet soil, and water samples. The brackets indicate the taxonomic name is contested, morphology-based taxonomy doesn’t always align with phylogeny

Fig. 5

Diversity along a latitudinal gradient is inverted for aquatic prokaryotes in vernal pools. The scatter plots show Shannon index (a) and Pielou’s evenness index (b) in vernal pools plotted across latitude (yellow dots)

Fig. 6

Dissimilarity in aquatic microbial communities in vernal pools increases with distance between sites; each point represents a specific value given by the Bray–Curtis dissimilarity index between two vernal pool microbial communities at varied distances