Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve
Shaw’s Agave is an endangered maritime succulent growing along the coast of California and northern Baja California. The population inhabiting Point Loma Peninsula (Naval Base, NB, and Cabrillo National Monument, CNM) has a complicated history of transplantation without documentation. Since 2008, there are no agave sprouts identified on the CNM site, and concerns have been raised about the genetic diversity of this population. We sequenced two barcoding loci, rbcL and matK, of 27 individual plants from 5 geographically distinct populations, including 12 individuals from California (NB and CNM). We also sampled soil from these plants for microbial and chemical analyses.
Unrooted phylogenetic tree of Shaw’s Agave generated in iTOL for rbcL and matK sequences. Sample names consist of geographic source (e.g., “CNM” or “NB”), plant identifier, and biological replicate (e.g., A/B/C). CNM = Cabrillo National Monument, NB = Point Loma Naval Base, BC = Border Fields, RS = Rosarito, and AH = Arroyo Hondo. (a) The suffix “R” in the above figure refers to the gene rbcL, while (b) the suffix “M” in the above figure refers to the gene matK. Phylogenetic trees were generated in Clustal Omega using neighbor-joining and further edited in the Interactive Tree of Life (iTOL). Radial bars represent evolutionary time distances from common ancestors. Synonymous–nonsynonymous analysis of (c) rbcL and (d) matK was performed for all sample pairs using SNAP v2.1.1.
Characteristics of Point Loma agave soil samples. Rows represent sample sites at Point Loma, and columns represent characteristics of soil. CNM = Cabrillo National Monument and NB = Point Loma Naval Base. Numbers (1–98) represent Agave shawii ssp. shawii individuals. Measurements of each chemical property (available in Table S4) were normalized to the highest value for that property and plotted. Green indicates relatively lower values, and red indicates relatively higher values.
Hierarchical clustering of microbial carbon source utilization profiles by sampling site. Rows represent single sampling events in Point Loma, and columns represent individual carbon sources. CNM = Cabrillo National Monument and NB = Point Loma Naval Base. Numbers (1–98) represent Agave shawii ssp. shawii individuals and A/B/C are biological replicates. Heatmap colors (green-red) represent normalized absorbance values postincubation normalized to preincubation absorbances and to the control well. Hierarchical clustering was generated in JMP Pro and Graphic. Carbon sources are labeled yellow (carbohydrates), green (polymers), purple (carboxylic and ketonic acids), black (amino acids), and blue (amine/amides).
Identified soil microbial species across Point Loma sites. A) Krona pie chart showing microbial taxon proportions from 16S rRNA sequences collected across all Point Loma sites (CNM and NB). This linked interactive version displays all identified microbial species data on lower taxonomic ranks. B) Bar chart showing the distribution of microbial phyla for each sampling site. The legend shows the top ten enriched phyla. C) Bar chart showing the distribution of microbial orders for each sampling site. The legend shows the top ten enriched orders.
Bray–Curtis dissimilarity NMDS plot between Cabrillo National Monument (CNM) and Point Loma Naval Base (NB) of agave sample sites based on 16S operational taxonomic unit (OTU) clustering: Beta diversity calculated by Bray–Curtis dissimilarity calculator between and among all agave sample sites on the California coast by microbial communities clustered in OTUs, with minimum confidence 97%. Numbers (1–98) represent Agave shawii ssp. shawii individuals. There is no significant clustering for each site.