Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

Abstract

Background: Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA.

Methods: We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites.

Results: Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism).

Discussion: Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.

Keywords: Edge effect; Eelgrass; Fragmentation; Microbiome; Rhizosphere; Seagrass; Sulfur metabolism.

Figure 1. Alpha diversity across samples.

Four alpha diversity metrics, observed number of OTUs, Chao1, the Shannon and Simpson diversity indices, are shown as boxplots for (A) different sample types (leaf, root, sediment) and for (B) sediment from different locations (inside, edge, outside).

Figure 2. Principal coordinates analysis (PCoA) of microbial communities based on weighted Unifrac distances.

Samples are colored by sample type (leaf, root, sediment) with different shapes for location (inside, edge, outside).

Figure 3. Principal coordinates analysis (PCoA) of microbial communities in sediment based on weighted Unifrac distances.

Samples are colored by location (inside, edge, outside).

Figure 4. Average relative abundance of taxonomic groups associated with each sample type (leaf, root, sediment).

OTUs are shown grouped by taxonomic order and colored by taxonomic class. Only orders with a mean abundance of at least one percent are shown here. The bars represent the standard error of the mean.

Figure 5. Average relative abundance of taxonomic groups associated with sediment from each location (inside, edge, outside).

Operational taxonomic units (OTUs) are shown grouped by taxonomic order and are colored by taxonomic class. Only orders with a mean relative abundance of at least one percent are shown. Bars represent the standard error of the mean.

Figure 6. Relationship between environmental data and microbial communities.

Non-metric multidimensional scaling (NMDS) of Bray Curtis dissimilarities of microbial communities found in sediment samples are shown here colored by location (inside, edge, outside). Environmental factors (p < 0.055, ANOVA) were overlaid as vectors onto the NMDS using the envfit function in vegan.