Brooke Weigel

All Publications

• Elevated light and CO2levels increase photosynthetic rates of diverse snow algal communities from the North Cascades. The New phytologist Weigel, B. L., Castillo, G., Pata, H. K., Young, J. N., Kodner, R. B. 2025

  Abstract

  Microalgae adapted to near-zero temperatures and high light levels live on snowfields and glaciers worldwide. Snow algae have red-colored pigments that darken snow surfaces, lowering its albedo and accelerating snowmelt. Despite their importance to the cryosphere, we know little about controls on snow algal productivity and biomass. Here, we characterize photophysiology from diverse natural field-collected populations of alpine snow algae from the North Cascades of Washington, USA, where the major red-bloom producing genera Chlainomonas, Sanguina, and Rosetta were present. We tested short-term physiological responses of snow algae to light (0-3000mumolm-2s-1) and CO2 levels (0-1600ppm), allowing us to determine the saturating light and CO2 levels for snow algal community net photosynthesis. All snow algal communities surveyed were adapted to extremely high light levels (3000mumolm-2s-1). In addition, photosynthesis rates of all the snow algal communities responded strongly to increasing CO2 levels. At current atmospheric CO2 levels (420ppm), snow algal net photosynthesis rates were only c. 50% saturated. Together, these results suggest the primary productivity of important bloom-forming snow algal communities in alpine ecosystems will likely rise as atmospheric CO2 concentrations increase, regardless of potential changes in available light levels.

  View details for DOI 10.1111/nph.70332

  View details for PubMedID 40598812

• Warming Seawater Temperature and Nutrient Depletion Alters Microbial Community Composition on a Foundational Canopy Kelp Species. Environmental microbiology Molnar, N. B., Weigel, B. L., Fales, R. J., Pfister, C. A. 2025; 27 (3): e70077

  Abstract

  Warming seawater temperatures and low dissolved inorganic nitrogen (DIN) levels are environmental stressors that affect the health and abundance of marine macroalgae and their microbiomes. Nereocystis luetkeana, a canopy-forming species of brown algae that forms critical habitat along the Pacific coast, has declined in regions impacted by these synergistic stressors. Little is known about how these environmental factors affect the microbiome of N. luetkeana, which could affect nutrient availability, vitamin production, and stress response for the host. We experimentally tested the interactive effects of three seawater temperatures (13°C, 16°C, 21°C) crossed with abundant and replete DIN levels on the diversity and composition of blade-associated microbiomes from two spatially separated kelp host populations. We hypothesised that kelp microbiomes exposed to high temperatures and low DIN would experience the lowest diversity. Contrary to our hypothesis, the highest temperature treatment resulted in the largest increase in microbial diversity, and microbiomes in all temperature treatments experienced a decrease in previously dominant taxa. Temperature had a larger effect than DIN on the kelp microbiome in all cases. The disruption to the kelp microbiome across all temperatures, especially at the highest temperature, suggests that the effects of warming on N. luetkeana extend to the microbiome.

  View details for DOI 10.1111/1462-2920.70077

  View details for PubMedID 40075558

  View details for PubMedCentralID PMC11903912

• Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp. Current biology : CB Bemmels, J. B., Starko, S., Weigel, B. L., Hirabayashi, K., Pinch, A., Elphinstone, C., Dethier, M. N., Rieseberg, L. H., Page, J. E., Neufeld, C. J., Owens, G. L. 2025; 35 (3): 688-698.e8

  Abstract

  Kelp forests are declining in many parts of the northeast Pacific.1,2,3,4 In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles,5,6,7 but natural selection may purge harmful variants.8,9,10 To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis sp.) from the coastlines of British Columbia and Washington. We identified 6 to 7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigor in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but these require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

  View details for DOI 10.1016/j.cub.2024.12.025

  View details for PubMedID 39826555

• Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California. Zootaxa Turner, T. L., Rouse, G. W., Weigel, B. L., Janusson, C., Lemay, M. A., Thacker, R. W. 2024; 5447 (1): 1-28

  Abstract

  This study presents a comprehensive taxonomic revision of the family Suberitidae (Porifera: Demospongiae) for California, USA. We include the three species previously known from the region, document two additional species previously known from other regions, and formally describe four new species as Pseudosuberites latke sp. nov., Suberites californiana sp. nov., Suberites kumeyaay sp. nov., and Suberites agaricus sp. nov. Multi-locus DNA sequence data is presented for seven of the nine species, and was combined with all publicly available data to produce the most comprehensive global phylogeny for the family to date. By integrating morphological and genetic data, we show that morphological characters may be sufficient for regional species identification but are likely inadequate for global classification into genera that reflect the evolutionary history of the family. We therefore propose that DNA sequencing is a critical component to support future taxonomic revisions.

  View details for DOI 10.11646/zootaxa.5447.1.1

  View details for PubMedID 39645850

• Interactive effects of temperature and nitrogen on the physiology of kelps (<i>Nereocystis luetkeana</i> and <i>Saccharina latissima</i>) FRONTIERS IN MARINE SCIENCE Fales, R. J., Weigel, B. L., Carrington, E., Berry, H. D., Dethier, M. N. 2023; 10

  View details for DOI 10.3389/fmars.2023.1281104

  View details for Web of Science ID 001123396400001

• Effects of temperature and nutrients on microscopic stages of the bull kelp (Nereocystis luetkeana, Phaeophyceae). Journal of phycology Weigel, B. L., Small, S. L., Berry, H. D., Dethier, M. N. 2023; 59 (5): 893-907

  Abstract

  Warming ocean temperatures have been linked to kelp forest declines worldwide, and elevated temperatures can act synergistically with other local stressors to exacerbate kelp loss. The bull kelp Nereocystis luetkeana is the primary canopy-forming kelp species in the Salish Sea, where it is declining in areas with elevated summer water temperatures and low nutrient concentrations. To determine the interactive effects of these two stressors on microscopic stages of N. luetkeana, we cultured gametophytes and microscopic sporophytes from seven different Salish Sea populations across seven different temperatures (10-22°C) and two nitrogen concentrations. The thermal tolerance of microscopic gametophytes and sporophytes was similar across populations, and high temperatures were more stressful than low nitrogen levels. Additional nitrogen did not improve gametophyte or sporophyte survival at high temperatures. Gametophyte densities were highest between 10 and 16°C and declined sharply at 18°C, and temperatures of 20 and 22°C were lethal. The window for successful sporophyte production was narrower, peaking at 10-14°C. Across all populations, the warmest temperature at which sporophytes were produced was 16 or 18°C, but sporophyte densities were 78% lower at 16°C and 95% lower at 18°C compared to cooler temperatures. In the field, bottom temperatures revealed that the thermal limits of gametophyte growth (18°C) and sporophyte production (16-18°C) were reached during the summer at multiple sites. Prolonged exposure of bull kelp gametophytes to temperatures of 16°C and above could limit reproduction, and therefore recruitment, of adult kelp sporophytes.

  View details for DOI 10.1111/jpy.13366

  View details for PubMedID 37497792

• The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes. mSystems Miranda, K., Weigel, B. L., Fogarty, E. C., Veseli, I. A., Giblin, A. E., Eren, A. M., Pfister, C. A. 2022; 7 (5): e0059222

  Abstract

  Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.

  View details for DOI 10.1128/msystems.00592-22

  View details for PubMedID 35993708

  View details for PubMedCentralID PMC9601103

• Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes. mSystems Weigel, B. L., Miranda, K. K., Fogarty, E. C., Watson, A. R., Pfister, C. A. 2022; 7 (3): e0142221

  Abstract

  Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.

  View details for DOI 10.1128/msystems.01422-21

  View details for PubMedID 35642511

  View details for PubMedCentralID PMC9238374

• Spatial organization of the kelp microbiome at micron scales. Microbiome Ramírez-Puebla, S. T., Weigel, B. L., Jack, L., Schlundt, C., Pfister, C. A., Mark Welch, J. L. 2022; 10 (1): 52

  Abstract

  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.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.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. Video abstract.

  View details for DOI 10.1186/s40168-022-01235-w

  View details for PubMedID 35331334

  View details for PubMedCentralID PMC8944128

• Differential impacts of alternate primary producers on carbon cycling. Ecology Miranda, K. K., Weigel, B. L., McCoy, S. J., Pfister, C. A. 2021; 102 (9): e03455

  Abstract

  Disturbance impacts the spatial distribution of primary producers, which can have cascading effects on ecosystem function. The lower-intertidal zone on the rocky shores of the Pacific Northwest is one such place where wave energy creates a mosaic-like distribution between two assemblages: surfgrass (Phyllospadix scouleri) meadows and macroalgal forests dominated by kelp. We simulated wave disturbance by experimentally removing patches of surfgrass monocultures, resulting in a macroalgal assemblage with increased diversity, biomass, and net primary productivity in the following year. Although surfgrass had a higher C:N compared to macroalgal assemblages, macroalgal assemblages achieved a higher biomass, fixed carbon at a faster rate, and released more dissolved organic carbon (DOC) during photosynthesis. Thus, despite similar standing amounts of carbon, macroalgal assemblages have increased carbon turnover-from fixation to DOC release. Comparative photophysiology indicated that surfgrasses have a competitive advantage over other macrophytes at low light levels, allowing them to persist when disturbance is reduced. Unexpectedly, disturbance in this system increased the potential for carbon sequestration when surfgrass monocultures were replaced by diverse macroalgae.

  View details for DOI 10.1002/ecy.3455

  View details for PubMedID 34166524

• Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLoS biology Davies, S. W., Putnam, H. M., Ainsworth, T., Baum, J. K., Bove, C. B., Crosby, S. C., Côté, I. M., Duplouy, A., Fulweiler, R. W., Griffin, A. J., Hanley, T. C., Hill, T., Humanes, A., Mangubhai, S., Metaxas, A., Parker, L. M., Rivera, H. E., Silbiger, N. J., Smith, N. S., Spalding, A. K., Traylor-Knowles, N., Weigel, B. L., Wright, R. M., Bates, A. E. 2021; 19 (6): e3001282

  Abstract

  Success and impact metrics in science are based on a system that perpetuates sexist and racist "rewards" by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals' meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change.

  View details for DOI 10.1371/journal.pbio.3001282

  View details for PubMedID 34129646

  View details for PubMedCentralID PMC8205123

• Oxygen metabolism shapes microbial settlement on photosynthetic kelp blades compared to artificial kelp substrates. Environmental microbiology reports Weigel, B. L., Pfister, C. A. 2021; 13 (2): 176-184

  Abstract

  We examined factors shaping community assembly of the bull kelp (Nereocystis luetkeana) microbiome by comparing microbial biofilm formation on photosynthetic kelp blade tissues and artificial kelp substrates ('agar substrates') deployed into a kelp forest. New kelp blade tissues were colonized by markedly distinct microbial taxa relative to agar substrates during the same time interval, even when agar substrates were infused with N. luetkeana blades, suggesting that microbial settlement onto kelp surfaces is more than just attraction to a polysaccharide-rich surface. Further, common seawater taxa such as Colwellia sp. and Psychromonas sp. became abundant on agar substrates but avoided new kelp blade tissues, indicating that host-specific factors may deter certain surface-associated marine microbial taxa. Over two-thirds of the bacterial taxa in the kelp microbiome were associated with strictly aerobic metabolisms; thus, photosynthetic production of O2 may favour aerobic microbial metabolisms. While living kelp blades primarily recruited aerobic microbes, including the obligate aerobe Granulosicoccus sp., microbes that colonized agar substrates were predominantly facultative anaerobes. We also found that infusion of kelp tissues into agar substrates altered microbial community composition and lowered taxonomic diversity relative to control agar substrates, suggesting that non-living components of the kelp blade also impact microbial community assembly.

  View details for DOI 10.1111/1758-2229.12923

  View details for PubMedID 33372322

• The dynamics and stoichiometry of dissolved organic carbon release by kelp. Ecology Weigel, B. L., Pfister, C. A. 2021; 102 (2): e03221

  Abstract

  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 (13 C) tracer method, we demonstrated that inorganic carbon is rapidly fixed and released by N. luetkeana blades as 13 DOC, within hours. However, recently fixed carbon (13 DOC) 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.

  View details for DOI 10.1002/ecy.3221

  View details for PubMedID 33048348

• Invertebrate grazing and epilithon assemblages control benthic nitrogen fixation in an N-limited river network FRESHWATER SCIENCE Weigel, B. L., Welter, J. R., Furey, P. C. 2020; 39 (3): 508-520

  View details for DOI 10.1086/710023

  View details for Web of Science ID 000563574700013

• Sea Cucumber Intestinal Regeneration Reveals Deterministic Assembly of the Gut Microbiome. Applied and environmental microbiology Weigel, B. L. 2020; 86 (14)

  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.

  View details for DOI 10.1128/AEM.00489-20

  View details for PubMedID 32358014

  View details for PubMedCentralID PMC7357475

• Kelp beds and their local effects on seawater chemistry, productivity, and microbial communities. Ecology Pfister, C. A., Altabet, M. A., Weigel, B. L. 2019; 100 (10): e02798

  Abstract

  Kelp forests are known as key habitats for species diversity and macroalgal productivity; however, we know little about how these biogenic habitats interact with seawater chemistry and phototroph productivity in the water column. We examined kelp forest functions at three locales along the Olympic Peninsula of Washington state by quantifying carbonate chemistry, nutrient concentrations, phytoplankton productivity, and seawater microbial communities inside and outside of kelp beds dominated by the canopy kelp species Nereocystis luetkeana and Macrocystis pyrifera. Kelp beds locally increased the pH, oxygen, and aragonite saturation state of the seawater, but lowered seawater inorganic carbon content and total alkalinity. Although kelp beds depleted nitrate and phosphorus concentrations, ammonium and dissolved organic carbon (DOC) concentrations were enhanced. Kelp beds also decreased chlorophyll concentrations and carbon fixed by phytoplankton, although kelp carbon fixation more than compensated for any difference in phytoplankton production. Kelp beds entrained distinct microbial communities, with higher taxonomic and phylogenetic diversity compared to seawater outside of the kelp bed. Kelp forests thus had significant effects on seawater chemistry, productivity and the microbial assemblages in their proximity. Thereby, the diversity of pathways for carbon and nitrogen cycling was also enhanced. Overall, these observations suggest that the contribution of kelp forests to nearshore carbon and nitrogen cycling is greater than previously documented.

  View details for DOI 10.1002/ecy.2798

  View details for PubMedID 31233610

• Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera. Frontiers in microbiology Weigel, B. L., Pfister, C. A. 2019; 10: 346

  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.

  View details for DOI 10.3389/fmicb.2019.00346

  View details for PubMedID 30863387

  View details for PubMedCentralID PMC6399156

• Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Scientific reports Weigel, B. L., Erwin, P. M. 2017; 7: 43247

  Abstract

  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 host-symbiont 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.

  View details for DOI 10.1038/srep43247

  View details for PubMedID 28233813

  View details for PubMedCentralID PMC5324122

• Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats. Applied and environmental microbiology Weigel, B. L., Erwin, P. M. 2016; 82 (2): 650-8

  Abstract

  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.

  View details for DOI 10.1128/AEM.02980-15

  View details for PubMedID 26567307

  View details for PubMedCentralID PMC4711132