Spatial organization of the kelp microbiome at micron scales

Abstract

Macroalgae are colonized by complex and diverse microbial communities that are distinct from those on inert substrates, suggesting intimate symbioses that likely play key roles in both macroalgal and bacterial biology. Canopy-forming kelp fix teragrams of carbon per year in coastal kelp forest ecosystems, yet little is known about the structure and development of their associated microbial communities. We characterized the spatial organization of bacterial communities on blades of the canopy-forming kelp Nereocystis luetkeana using fluorescence in situ hybridization and spectral imaging with a probe set combining phylum, class and genus-level probes to target >90% of the microbial community. We show that kelp blades host a dense microbial biofilm, generally less than 20 m thick, in which disparate microbial taxa live in close contact with one another. The biofilm is spatially differentiated, with tightly 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. Further, a community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial community structure and cell density increased 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. Finally, kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population, indicating that biofilms are characteristic of health and that biofilm loss may be related to the condition of the host. ImportanceThe microbial community coating the surfaces of macroalgae may play a key but underexplored role both in the biology of the macroalgal host and in the biogeochemistry of the coastal ocean. We show that photosynthetic blades of the canopy-forming kelp Nereocystis luetkeana host a complex microbial biofilm that is both dense and spatially differentiated. Microbes of different taxa are in intimate cell-to-cell contact with one another; microbial cells invade the interior of kelp cells as well as cover their external surfaces; and a subset of the surface microbiota projects into the water column. These results highlight the potential for metabolic interactions between key members of the kelp microbiome as well as between microbes and their host. The dense layer of microbes 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.