Spatial organization of the kelp microbiome at micron scales

Abstract

Background Elucidating the spatial structure of host-associated microbial communities is essential for understanding taxon-taxon interactions within the microbiota and between microbiota and host. Macroalgae are colonized by complex microbial communities, suggesting intimate symbioses that likely play key roles in both macroalgal and bacterial biology, yet little is known about the spatial organization of microbes associated with macroalgae. Canopy-forming kelp are ecologically significant, fixing teragrams of carbon per year in coastal kelp forest ecosystems. We characterized the micron-scale spatial organization of bacterial communities on blades of the kelp Nereocystis luetkeana using fluorescence in situ hybridization and spectral imaging with a probe set combining phylum-, class-, and genus-level probes to localize and identify > 90% of the microbial community. Results We show that kelp blades host a dense microbial biofilm composed of disparate microbial taxa in close contact with one another. The biofilm is spatially differentiated, with clustered cells of the dominant symbiont Granulosicoccus sp. (Gammaproteobacteria) close to the kelp surface and filamentous Bacteroidetes and Alphaproteobacteria relatively more abundant near the biofilm-seawater interface. A community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial cell density increased markedly along the length of the kelp blade, from sparse microbial colonization of newly produced tissues at the meristematic base of the blade to an abundant microbial biofilm on older tissues at the blade tip. Kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population. Conclusions Imaging revealed close association, at micrometer scales, of different microbial taxa with one another and with the host. This spatial organization creates the conditions necessary for metabolic exchange among microbes and between host and microbiota, such as provisioning of organic carbon to the microbiota and impacts of microbial nitrogen metabolisms on host kelp. The biofilm coating the surface of the kelp blade is well-positioned to mediate interactions between the host and surrounding organisms and to modulate the chemistry of the surrounding water column. The high density of microbial cells on kelp blades (105–107 cells/cm2), combined with the immense surface area of kelp forests, indicates that biogeochemical functions of the kelp microbiome may play an important role in coastal ecosystems.

Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes

“…Bold numbers in parentheses indicate the number of unique genes associated with each function. (B) Image of the micrometer-scale spatial structure of the N. luetkeana surface microbiome depicting clusters of magenta Granulosicoccus cells (coccus shaped), adapted with permission from the work of Ramírez-Puebla et al ( 5 ).…”

“…MAGs persisted spatially as well as temporally, with 15 MAGs (23% of the total) detected on bull kelp from Tatoosh and Squaxin populations, which are separated by the length of Puget Sound and the Strait of Juan de Fuca (~300 km). Kelp from Squaxin Island have lower bacterial cell abundances ( 5 ) and a different composition of microbes than do kelp from Tatoosh Island ( 9 ). Here, we found that Granulosicoccus was the most abundant MAG at both sites in 2019.…”

“…The genus Granulosicoccus (order Chromatiales , class Gammaproteobacteria ) currently contains 4 species isolated from Antarctic seawater ( 67 , 68 ), the seagrass Zostera marina ( 69 ), and the kelp Undaria pinnatifida ( 70 ). Granulosicoccus is the most abundant bacterium associated with N. luetkeana ( 9 ), reaching densities of up to 10 6 cells per cm 2 on kelp blades ( 5 ), and it associates with diverse algal hosts ( 18 ). Only a single annotated genome is available for this bacterial genus, belonging to the free-living Granulosicoccus antarcticus type strain IMCC3135 ( 37 ).…”

“…Canopy-forming kelp species create structural habitat in temperate and arctic coastal regions worldwide ( 3 ). Photosynthetic kelp blades are covered by a dense and diverse microbiome, with up to 10 7 bacterial cells per cm 2 of kelp tissue ( 4 , 5 ). Microbes associated with large habitat-forming organisms can directly influence ecosystem-level biogeochemical cycles ( 6 ), yet we know little about the functional role of the kelp microbiome.…”

“…Here, we used a genome-resolved metagenomics approach to determine the functional roles and metabolic capabilities of bacterial symbionts associated with photosynthetic blades of the canopy-forming bull kelp ( Nereocystis luetkeana ). The bull kelp microbiome is comprised of a few microbial taxa that persist across geographic locations ( 9 ), colonize new tissues rapidly ( 30 ), reach high cell densities, and display repeatable micrometer-scale spatial structure ( 5 ). We reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from bull kelp blade tissues, spanning 6 bacterial phyla and 19 families.…”