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.

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Our research showed that kelp beds locally increased the pH, oxygen, and aragonite saturation state of the seawater, while seawater inorganic carbon content and total alkalinity were lowered. Kelp beds depleted nitrate and phosphorus concentrations, but enhanced ammonium and DOC concentrations. Kelp beds entrained distinct microbial communities, with higher taxonomic and phylogenetic diversity compared to seawater outside of the kelp bed, and kelp carbon fixation more than compensated for decreased phytoplankton production that occurred in their proximity. Thus, the diversity of pathways for carbon and nitrogen cycling is enhanced in proximity to kelp.Pfister, C. A., M. A.

Canopy‐forming kelps are foundational species in coastal ecosystems, fixing tremendous amounts of carbon, yet we know little about the ecological and physiological determinants of dissolved organic carbon (DOC) release by kelps. We examined DOC release by the bull kelp, Nereocystis luetkeana, in relation to carbon fixation, nutrient uptake, tissue nitrogen content, and light availability. DOC release was approximately 3.5 times greater during the day than at night. During the day, N. luetkeana blades released an average of 16.2% of fixed carbon as DOC. Carbon fixation increased with light availability but DOC release did not, leading to a lower proportion of fixed carbon released as DOC at high light levels. We found no relationship between carbon fixation and DOC release rates measured concurrently. Rather, DOC release by N. luetkeana blades declined with marginal significance as blade tissue nitrogen content increased and with experimental nitrate addition, supporting the role of stoichiometric relationships in DOC release. Using a stable isotope (13C) tracer method, we demonstrated that inorganic carbon is rapidly fixed and released by N. luetkeana blades as 13DOC, within hours. However, recently fixed carbon (13DOC) comprised less than 20% of the total DOC released, indicating that isotope studies that rely on tracer production alone may underestimate total DOC release, as it is decoupled from recent kelp productivity. Comparing carbon and nitrogen assimilation dynamics of the annual kelp N. luetkeana with the perennial kelp Macrocystis pyrifera revealed that N. luetkeana had significantly higher carbon fixation, DOC production and nitrogen uptake rates per unit dry mass. Both kelp species were able to perform light‐independent carbon fixation at night. Carbon fixation by the annual kelp N. luetkeana is as high as 2.35 kg C·m−2·yr−1, but an average of 16% of this carbon (376 g C·m−2·yr−1) is released as DOC. As kelp forests are increasingly viewed as vehicles for carbon sequestration, it is important to consider the fate of this substantial quantity of DOC released by canopy‐forming kelps.

Sponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidal Hymeniacidon heliophila sponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared to H. heliophila symbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found in H. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses. Sponges form ancient symbioses (as described in reference 1) with a great diversity of bacterial, archaeal, and eukaryotic microorganisms (1, 2). Most of these microbial symbionts elude cultivation (3); thus, culture-independent techniques such as next-generation DNA sequencing are necessary to elucidate the immense diversity of microbial communities in marine sponges. For example, the sponge Rhopaloeides odorabile hosts nearly 3,000 unique microbial taxa (4). Symbiotic microbes can constitute up to 40% of the sponge mesohyl volume (5) and perform a variety of ecological functions in the host sponge (6). Sponge-associated microbial symbionts may play roles in the nutrient acquisition, chemical defense production, antifouling activity, and disease susceptibility of host sponges (1, 7). Despite the ubiquity of microbial symbionts in sponges, much is still unknown about their structure and ecological function.Sponges host microbial communities that are distinct from those found in seawater and exhibit a high degree of host specificity (4, 8, 9), even between closely related sponge species (10). Determining what structures these symbiotic communities is a current research priority, because it will provide insight into the maintenance of one of the most ancient metazoan-microbial symbio...

Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in hostsymbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.Microorganisms influence many aspects of multicellular life, including the maintenance of genetic diversity through horizontal gene transfer, pathogenesis, provisioning of resources through nutrient cycling, and the acquisition of novel traits or resources via symbiotic associations 1 . Despite the widespread occurrence of animal-microbe associations among taxonomically diverse hosts and symbionts, the maintenance of these symbiotic associations across space and time is just beginning to be understood. Microbial symbionts in sponges (phylum Porifera) are ubiquitous, forming complex and host-specific communities that can contain thousands of unique microbial taxa 2,3 . Symbiotic microorganisms may benefit the sponge holobiont through photosynthesis 4,5 , nitrogen cycling 6-8 , hydrogen sulfide oxidation 9 , and the production of bioactive secondary metabolites 10 . Host specificity plays a major role in structuring symbiont communities, with many studies demonstrating substantial differences in microbial community structure and composition among different sponge species [11][12][13][14] . While interspecific variation in sponge-associated microbial communities is well established, relatively little is known about intraspecific variation in the sponge microbiome.Spatial and temporal stability of sponge-microbe associations have been commonly reported. Bacterial symbionts of Mediterranean Ircinia spp. displayed temporal stability over 1.5 years 15 , spatial stability across distances of up to 800 ...

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.

ABSTRACT The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber Sclerodactyla briareus, and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens. IMPORTANCE The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) Sclerodactyla briareus was explored as an experimental system to study microbial colonization in the gut, as S. briareus individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.