Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera

Abstract

Canopy-forming kelps create underwater forests that are among the most productive marine ecosystems. On the Pacific coast of North America, two canopy-forming kelps with contrasting life histories co-occur; Macrocystis pyrifera, a perennial species, and Nereocystis luetkeana, an annual species. Kelp blade-associated microbes were sampled from 12 locations across a spatial gradient in Washington, United States, from the outer Pacific Coast to Puget Sound. Microbial communities were characterized using next-generation Illumina sequencing of 16S rRNA genes. At higher taxonomic levels (bacterial phylum and class), canopy-forming kelps hosted remarkably similar microbial communities, but at the amplicon sequence variant level, microbial communities on M. pyrifera and N. luetkeana were host-specific and distinct from free-living bacteria in the surrounding seawater. Microbial communities associated with blades of each kelp species displayed significant geographic variation. The microbiome of N. luetkeana changed along the spatial gradient and was significantly correlated to salinity, with outer Pacific coast sites enriched in Bacteroidetes (family Saprospiraceae) and Gammaproteobacteria (Granulosicoccus sp.), and southern Puget Sound sites enriched in Alphaproteobacteria (family Hyphomonadaceae). We also examined microbial community development and succession on meristematic and apical N. luetkeana blade tissues throughout the summer growing season on Tatoosh Island, WA. Across all dates, microbial communities were less diverse on younger, meristematic blade tissue compared to the older, apical tissues. In addition, phylogenetic relatedness among microbial taxa increased from meristematic to apical blade tissues, suggesting that the addition of microbial taxa to the community was a non-random process that selected for certain phylogenetic groups of microbes. Microbial communities on older, apical tissues displayed significant temporal variation throughout the summer and microbial taxa that were differentially abundant over time displayed clear patterns of community succession. Overall, we report that host species identity, geographic location, and blade tissue age shape the microbial communities on canopy-forming kelps.

Keywords: Macrocystis; Nereocystis; biogeography; community succession; holobiont; kelp; microbial symbiont; microbiome.

FIGURE 1

Map of kelp forests sampled in Washington, including co-occurring N. luetkeana and M. pyrifera kelp forests (pink circles) and locations where only N. luetkeana was sampled (green circles). The filled circles indicate kelp forests that were sampled for geographic comparisons (n = 12), while the green star indicates the location of Tatoosh Island, where temporal sampling was conducted.

FIGURE 2

Alpha diversity indices including (A) mean ASV count, (B) mean Shannon diversity, (C) mean Faith’s phylogenetic diversity, and (D) mean Pielou’s evenness for N. luetkeana, M. pyrifera, and seawater microbial communities.

FIGURE 3

Non-metric multidimensional scaling plot of M. pyrifera, N. luetkeana, and seawater microbial communities across 12 sites in Washington.

FIGURE 4

Relative abundance barplots of kelp blade microbial communities from N. luetkeana (top row) and M. pyrifera (bottom row) across 11 and 5 sites, respectively. Colors represent bacterial orders classified by Silva taxonomy. Sites are listed from left to right in order of decreasing ocean influence, from the outer coast (Destruction Island, Cape Johnson, Cape Alava, and Koitlah) to the Strait of Juan de Fuca (Sekiu, Freshwater Bay, and Port Townsend) and Puget Sound (Scatchet Whidbey, Shilshole Seattle, Tacoma Narrows, and Squaxin Island).

FIGURE 5

(A) Mean (±standard error) length of sampled blades and (B) mean (±standard error) linear blade growth rates throughout the growing season.

FIGURE 6

Heatmap showing the relative abundances of the 100 most abundant bacterial ASVs from N. luetkeana blade meristem, blade tip, and surrounding seawater microbial communities.

FIGURE 7

Alpha diversity indices including (A) mean (±standard error) ASV count, (B) mean (±standard error) Shannon diversity, (C) mean (±standard error) Faith’s phylogenetic diversity, and (D) mean (±standard error) Pielou’s evenness for N. luetkeana blade meristem (light green) and blade tip (dark green) microbial communities throughout the growing season.

FIGURE 8

Principal coordinate analysis (PCoA) plot of all N. luetkeana microbial communities across 12 sites in Washington, combining the N. luetkeana mid-blade samples from the geographic sampling (squares) with the temporal dataset from Tatoosh Island, WA (black circles = N. luetkeana blade meristem, black triangles = N. luetkeana blade tip).

FIGURE 9

Mean abundances of ASVs (n = 40) from N. luetkeana blade tip microbial communities that displayed significantly different abundances across time with ANCOM. The ASVs that displayed significant temporal patterns were classified as early, mid, and late successional taxa based on when they were most abundant in blade tip communities. Each ASV is plotted individually and colored by bacterial class.

FIGURE 10

Mean (±standard error) (A) nearest taxon index and (B) NRI of microbial communities on N. luetkeana blade meristem (n = 30), N. luetkeana blade tip (n = 36), and surrounding seawater samples (n = 22) from Tatoosh Island, WA.