15.Chen, MY; Fulton, LM; Huang, IV; Liman, A; Hossain, SS; Hamilton, CD; Song, SY; Geissmann, Q; King, KC; Haney, CH. (2025) Order among chaos: High throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system.PLoS Pathog. 21 Order among chaos: High throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system
The likelihood that a host will be susceptible to infection is influenced by the interaction of diverse biotic and abiotic factors. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between the host, the environment, and biotic factors such as the microbiome. For example, pathogen infection success is known to vary by host genotype, bacterial strain identity and dose, and pathogen dose. Elucidating the interactions between these factors in vivo has been challenging because testing combinations of these variables quickly becomes experimentally intractable. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, non-pathogenic bacteria, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbe model, we found that host genotype and bacterial strain order of arrival predict host susceptibility to infection, but pathogen and non-pathogenic bacterial dose can overwhelm these effects. Host susceptibility to infection is therefore driven by complex interactions between multiple factors that can both mask and compensate for each other. However, regardless of host or inoculation conditions, the ratio of pathogen to non-pathogen emerged as a consistent correlate of disease. Our results demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host susceptibility to disease. Increasing the scale at which we can screen drivers of disease, such as microbiome community structure, will facilitate both disease predictions and treatments for medicine and agricultural applications. DOI
14. Moreira, ZPM; Kak, K; Wei, ZW; Yanez-Ortuno, D; Wang, NR; Hedges, JB; Chen, MY; Geissmann, Q; Zhang, WT; Chatterton, S; Ryan, KS; Haney, CH. (2025) Azomycin produced by Pseudomonas has both phytotoxic and anti-oomycete activity.J. Bacteriol.Azomycin produced by Pseudomonas has both phytotoxic and anti-oomycete activity
root rot; <italic>Aphanomyces euteiches</italic>; nitroimidazole antibiotics; <italic>Pisum sativum</italic>
Members of the genus Pseudomonas synthesize diverse natural products that contribute to their versatility in free-living and host-associated lifestyles. Here, we characterized the in vivo functions of the nitroimidazole antibiotic azomycin in the genus Pseudomonas. We found that genes with similarity to azomycin biosynthesis genes rohPQRST are prevalent within the Pseudomonas syringae species complex and rarely present in the Pseudomonas fluorescens species complex. Azomycin production was detectable in culture by biocontrol strains Pseudomonas spp. DF41 and CMR5a. Pseudomonas sp. DF41 exhibited anti-oomycete activity that was lost in a triangle rohPQRST mutant. Purified azomycin was sufficient to kill the oomycete pathogens Aphanomyces and Phytophthora. Although DF41 has been studied for its role in biocontrol of plant pathogens, we found that azomycin exhibited phytotoxicity against Pisum sativum (pea) plants at similar concentrations to those that inhibited oomycetes. However, consistent with its use as a biocontrol agent, Pseudomonas sp. DF41 only produced azomycin in planta when pea plants were infected with the oomycete pathogen Aphanomyces euteiches. Our findings suggest dual roles for azomycin in Pseudomonas, functioning both as a biocontrol agent of oomycete pathogens, as well as a phytotoxic molecule with a potential role in plant virulence.IMPORTANCEWhile many natural products are studied for their roles in the treatment of plant or human disease, the ecological functions of natural products are understudied. We found that an antibiotic, azomycin, is produced by Pseudomonas species and has toxicity against both plants and oomycete pathogens. Our findings suggest a complex ecological role of azomycin production by Pseudomonas in both the amelioration and exacerbation of plant disease. DOI
13. Song, SY; McDonald, KJ; Bhat, A; Chen, MY; Moreira, ZM; Haney, CH. (2025) FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome.Mol. Plant-Microbe Interact.FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome
FER; LRX; pH stress; plant-microbiome interactions; rhizosphere microbiome
Plants establish beneficial associations with microbiota, enhancing their resilience to environmental challenges. FERONIA (FER) kinase shapes the microbiome; despite extensive knowledge of FER interactors that regulate development and immunity against pathogens, the specific partners involved in microbiome modulation remain underexplored. Through a reverse genetic screen of Arabidopsis leucine-rich repeat extensin (LRX) genes, which encode FER-interacting cell wall sensors, we found that loss of function of lrx1/2 leads to enriched rhizosphere Pseudomonas, similar to fer mutants. 16S rRNA sequencing revealed that, when grown in natural soil, lrx1/2 and fer-4 have similarly altered rhizosphere microbiomes with decreased bacterial diversity. Notably, lrx1/2 and fer-4 mutants both exhibit growth defects in high pH natural soil that could be rescued by lowering the soil pH and increasing phosphate. Microbiome sequencing under conditions that rescued fer-4 and lrx1/2 stunting showed that the altered microbiome of lrx1/2 and fer-4 persists independently of changes in plant growth. This indicates that FER and LRX1/2 play an integral role in shaping the rhizosphere microbiome.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license. DOI
12. Thoms, D; Chen, MY; Liu, Y; Fulton, L; Luo, YQ; Hiott, DE; Song, SY; Moreira, ZM; Wang, NR; Zorio, D; Rejzek, M; Potter, R; Carella, P; Haney, CH. (2025) A bacterial exotoxin-triggered plant immune response restricts pathogen growth.Cell Reports 44 A bacterial exotoxin-triggered plant immune response restricts pathogen growth
For optimal growth and development, hosts must promote healthy symbiotic interactions while restricting pathogens. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant root-associated strains within the Pseudomonas fluorescens species complex. Despite having similar immunogenic microbe-associated molecular patterns, one strain is beneficial and the other exhibits exotoxin-dependent virulence. We show that the two strains co-exist in vitro, but the beneficial strain outcompetes the pathogen in the rhizosphere. We find that plants respond to the pathogen, but not the beneficial strain, predominantly via an exotoxin-triggered defense response in roots. The purified exotoxin is sufficient to induce immunity and restrict bacterial growth in a BAK1/BKK1/CERK1-dependent manner. We show that these immune components are also required for balancing the growth between the beneficial and pathogenic strains. We conclude that plant immunity can distinguish phylogenetically similar microbes with distinct lifestyles, in part, through perception of exotoxins. DOI
11. Yanez Ortuno D, Chen MY, McDonald K, Gacad A, Carrillo J, Haney CH. (2025) Predicting bacterial-mediated entomopathogenicity through comparative genomics and statistical modeling.Microbiol Spectr 0:e03108-25. Predicting bacterial-mediated entomopathogenicity through comparative genomics and statistical modeling.
Bacterial genomes encode vast functional diversity and have both beneficial and detrimental effects on insect hosts. While genotype-to-phenotype relationships are known for specific insecticidal genes on individual insect hosts, whether these mechanisms will be effective on a phylogenetically distinct insect host is not always known. To determine if known virulence genes are effective on a new host, we developed a method to merge existing mechanistic knowledge with in vivo tests on a small number of bacterial isolates to predict bacterial genes associated with entomopathogenesis. We used a model consisting of Drosophila melanogaster interactions with pathogenic and commensal genome-sequenced strains of Pseudomonas bacteria. We compiled a database of previously described insecticidal and biocontrol genes within the Pseudomonas genus and used comparative genomics to probe the distribution of these genes across Pseudomonas strains. We found natural variation in the presence of known insecticidal genes across the genus. We tested the insect-killing capacity of 13 Pseudomonas spp. strains against D. melanogaster and found natural variation in insecticidal activity. To identify bacterial genes associated with fly mortality, we employed two statistical models to correlate bacterial virulence with the presence of previously described insecticidal activity. To validate our predictions, we used a P. aeruginosa PAO1 transposon mutant library and identified eight operons that are necessary for killing D. melanogaster. We show that by combining existing literature with phenotyping a small number of strains, we identified both known and novel genes associated with insecticidal activity in D. melanogaster, using a rapid, scalable screening framework. More broadly, these findings illustrate a discovery pipeline for bacterial virulence mechanisms, accelerating the discovery of insect pest biocontrol mechanisms. DOI
10. Yang Liu, Alexandra D Gates, Zhexian Liu, Quinn Duque, Sierra S Schmidt, Melissa Y Chen, Corri D Hamilton, George A O’Toole, Cara H Haney. (2025) In vitro biofilm formation by a beneficial bacterium partially predicts in planta protection against rhizosphere pathogens.The ISME JournalIn vitro biofilm formation by a beneficial bacterium partially predicts in planta protection against rhizosphere pathogens
Plant roots form associations with beneficial and pathogenic soil microorganisms. Although members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas brassicacearum WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen Pseudomonas sp. N2C3 and confers protection against N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. brassicacearum WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased biofilm on abiotic surfaces, respectively. We found that whereas the P. brassicacearum WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants lost protection against N2C3. Non-protective mutants those involved in large adhesion protein (LapA) biosynthesis, flagellar synthesis and function, and O-antigen biosynthesis. We found that the inability of P. brassicacearum WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions. DOI
9. Alexiev, A; Chen, MY; Korpita, T; Weier, AM; McKenzie, VJ. (2023) Together or Alone: Evaluating the Pathogen Inhibition Potential of Bacterial Cocktails against an Amphibian Pathogen.Microbiol. Spectr. 11 Together or Alone: Evaluating the Pathogen Inhibition Potential of Bacterial Cocktails against an Amphibian Pathogen
Anaxyrus boreas boreas; Janthinobacterium lividum; Batrachochytrium dendrobatidis; boreal toad; multistrain; probiotics
Batrachochytrium dendrobatidis (Bd) is a pathogen that infects amphibians globally and is causing a biodiversity crisis. Our research group studies one of the species affected by Bd, namely, the Colorado boreal toad (Anaxyrus boreas boreas). The amphibian fungal skin disease Batrachochytrium dendrobatidis (Bd) has caused major biodiversity losses globally. Several experimental trials have tested the use of Janthinobacterium lividum to reduce mortality due to Bd infections, usually in single-strain amendments. It is well-characterized in terms of its anti-Bd activity mechanisms. However, there are many other microbes that inhibit Bd in vitro, and not all experiments have demonstrated consistent results with J. lividum. We used a series of in vitro assays involving bacterial coculture with Bd lawns, bacterial growth tests in liquid broth, and Bd grown in bacterial cell-free supernatant (CFS) to determine: (i) which skin bacteria isolated from a locally endangered amphibian, namely, the Colorado boreal toad (Anaxyrus boreas boreas), are able to inhibit Bd growth; (ii) whether multistrain combinations are more effective than single-strains; and (iii) the mechanism behind microbe-microbe interactions. Our results indicate that there are some single strain and multistrain probiotics (especially including strains from Pseudomonas, Chryseobacterium, and Microbacterium) that are potentially more Bd-inhibitive than is J. lividum alone and that some combinations may lead to a loss of inhibition, potentially through antagonistic metabolite effects. Additionally, if J. lividum continues being developed as a wild boreal toad probiotic, we should investigate it in combination with Curvibacter CW54D, as they inhibited Bd additively and grew at a higher rate when combined than did either alone. This highlights the fact that combinations of probiotics function in variable and unpredictable ways as well as the importance of considering the potential for interactions among naturally resident host microbiota and probiotic additions.IMPORTANCE Batrachochytrium dendrobatidis (Bd) is a pathogen that infects amphibians globally and is causing a biodiversity crisis. Our research group studies one of the species affected by Bd, namely, the Colorado boreal toad (Anaxyrus boreas boreas). Many researchers focus their studies on one probiotic bacterial isolate called Janthinobacterium lividum, which slows Bd growth in lab cultures and is currently being field tested in Colorado boreal toads. Although promising, J. lividum is not consistently effective across all amphibian individuals or species. For Colorado boreal toads, we addressed whether there are other bacterial strains that also inhibit Bd (potentially better than does J. lividum) and whether we can create two-strain probiotics that function better than do single-strain probiotics. In addition, we evaluate which types of interactions occur between two-strain combinations and what these results mean in the context of adding a probiotic to an existing amphibian skin microbiome. DOI
8.Chen, MY; Haney, CH. (2023) It takes a plant village to raise a microbiome.Cell Host Microbe 31: 1956-1958 It takes a plant village to raise a microbiome
In this issue of Cell Host and Microbe, Meyer et al. explore the effects of host history on the inheritance of the plant microbiome. They find that transmission from the same plant species resulted in microbiota specialization, while transmission from a different species resulted in host generalism. DOI
7. Moreira, ZPM; Chen, MY; Ortuno, DLY; Haney, CH. (2023) Engineering plant microbiomes by integrating eco- evolutionary principles into current strategies.Curr. Opin. Plant Biol. 71 Engineering plant microbiomes by integrating eco- evolutionary principles into current strategies
Genome-wide association studies; SynComs; Rhizosphere; Phyllo- sphere; Legacy effects; Soil amendments
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome en-gineering efforts so as not to introduce off-target negative ef-fects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches. DOI
6.Chen, MY; Alexiev, A; McKenzie, VJ. (2022) Bacterial Biofilm Thickness and Fungal Inhibitory Bacterial Richness Both Prevent Establishment of the Amphibian Fungal Pathogen Batrachochytrium dendrobatidis.Appl. Environ. Microbiol. 88 Bacterial Biofilm Thickness and Fungal Inhibitory Bacterial Richness Both Prevent Establishment of the Amphibian Fungal Pathogen Batrachochytrium dendrobatidis
biofilms; fungal-bacterial interactions; pathogens; microbial ecology fungi
Host-associated microbial biofilms can provide protection against pathogen establishment. In many host-microbe symbioses (including, but not limited to humans, plants, insects, and amphibians), there is a correlation between host-associated microbial diversity and pathogen infection risk. Diversity may prevent infection by pathogens through sampling effects and niche complementarity, but an alternative hypothesis may be that microbial biomass is confounded with diversity and that host-associated biofilms are deterring pathogen establishment through space preemption. In this study, we use the amphibian system as a model for host-microbe-pathogen interactions to ask two questions: (i) is bacterial richness confounded with biofilm thickness or cell density, and (ii) to what extent do biofilm thickness, cell density, and bacterial richness each deter the establishment of the amphibian fungal pathogen Batrachochytrium dendrobatidis? To answer these questions, we built a custom biofilm microcosm that mimics the host-environment interface by allowing nutrients to diffuse out of a fine-pore biofilm scaffolding. This created a competitive environment in which bacteria and the fungal pathogen compete for colonization space. We then challenged bacterial biofilms ranging in community richness, biofilm thickness, bacterial cell density, and B. dendrobatidis (also known as Bd)-inhibitory metabolite production with live B. dendrobatidis zoospores to determine how B. dendrobatidis establishment success on membranes varies. We found that biofilm thickness and B. dendrobatidis-inhibitory isolate richness work in complement to reduce B. dendrobatidis establishment success. This work underscores that physical aspects of biofilm communities can play a large role in pathogen inhibition, and in many studies, these traits are not studied. IMPORTANCE Our finding highlights the fact that diversity, as measured through 165 rRNA gene sequencing, may obscure the true mechanisms behind microbe-mediated pathogen defense and that physical space occupation by biofilm-forming symbionts may significantly contribute to pathogen protection. These findings have implications across a wide range of host-microbe systems since 165 rRNA gene sequencing is a standard tool used across many microbial systems. Further, our results are potentially relevant to many host-pathogen systems since host-associated bacterial biofilms are ubiquitous. DOI
5.Chen, MY; Kueneman, JG; González, A; Humphrey, G; Knight, R; McKenzie, VJ. (2022) Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians.Mol. Ecol. 31: 2140-2156 Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians
amphibians; bacteria; community ecology; disease biology fungi
Pathogen success (risk and severity) is influenced by host-associated microbiota, but the degree to which variation in microbial community traits predict future infection presence/absence (risk) and load (severity) for the host is unknown. We conducted a time-series experiment by sampling the skin-associated bacterial communities of five amphibian species before and after exposure to the fungal pathogen, Batrachochytrium dendrobaditis (Bd). We sought to determine whether microbial community traits are predictors of, or are affected by, Bd infection risk and intensity. Our results show that richness of putative Bd-inhibitory bacteria strongly predicts infection risk, while the proportion of putative Bd-inhibitory bacteria predicts future infection intensity. Variation in microbial community composition is high across time and individual, and bacterial prevalence is low. Our findings demonstrate how ecological community traits of host-associated microbiota may be used to predict infection risk by pathogenic microbes. DOI
4. Li, DJ; Record, S; Sokol, ER; Bitters, ME; Chen, MY; Chung, YA; Helmus, MR; Jaimes, R; Jansen, L; Jarzyna, MA; Just, MG; LaMontagne, JM; Melbourne, BA; Moss, W; Noman, KEA; Parker, SM; Robinson, N; Seyednasroliah, B; Smith, C; Spaulding, S; Surasinghe, TD; Thomsen, SK; Zarnetske, PL. (2022) Standardized NEON organismal data for biodiversity research.Ecosphere 13 Standardized NEON organismal data for biodiversity research
biodiversity; data package; data product; EDI; organismal data; R; Special Feature; Harnessing the NEON Data Revolution
Understanding patterns and drivers of species distribution and abundance, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high-quality, empirical data that span large spatial scales and long time periods. The NEON fills this gap by providing freely available observational data that are generated during robust and consistent organismal sampling of several sentinel taxonomic groups within 81 sites distributed across the United States and will be collected for at least 30 years. The breadth and scope of these data provide a unique resource for advancing biodiversity research. To maximize the potential of this opportunity, however, it is critical that NEON data be maximally accessible and easily integrated into investigators' workflows and analyses. To facilitate its use for biodiversity research and synthesis, we created a workflow to process and format NEON organismal data into the ecocomDP (ecological community data design pattern) format that were available through the ecocomDP R package; we then provided the standardized data as an R data package (neonDivData). We briefly summarize sampling designs and data wrangling decisions for the major taxonomic groups included in this effort. Our workflows are open-source so the biodiversity community may: add additional taxonomic groups; modify the workflow to produce datasets appropriate for their own analytical needs; and regularly update the data packages as more observations become available. Finally, we provide two simple examples of how the standardized data may be used for biodiversity research. By providing a standardized data package, we hope to enhance the utility of NEON organismal data in advancing biodiversity research and encourage the use of the harmonized ecocomDP data design pattern for community ecology data from other ecological observatory networks. DOI
3. Alexiev, A; Chen, MLY; McKenzie, VJ. (2021) Identifying fungal-host associations in an amphibian host system.PLoS One 16 Identifying fungal-host associations in an amphibian host system
fungi
Host-associated microbes can interact with macro-organisms in a number of ways that affect host health. Few studies of host-associated microbiomes, however, focus on fungi. In addition, it is difficult to discern whether a fungal organism found in or on an ectotherm host is associating with it in a durable, symbiotic interaction versus a transient one, and to what extent the habitat and host share microbes. We seek to identify these host-microbe interactions on an amphibian, the Colorado boreal toad (Anaxyrus boreas boreas). We sequenced the ITS1 region of the fungal community on the skin of wild toads (n = 124) from four sites in the Colorado Rocky Mountains, across its physiologically dynamic developmental life stages. We also sampled the common habitats used by boreal toads: water from their natal wetland and aquatic pond sediment. We then examined diversity patterns within different life stages, between host and habitat, and identified fungal taxa that could be putatively host-associated with toads by using an indicator species analysis on toad versus environmental samples. Host and habitat were strikingly similar, with the exception of toad eggs. Post-hatching toad life stages were distinct in their various fungal diversity measures. We identified eight fungal taxa that were significantly associated with eggs, but no other fungal taxa were associated with other toad life stages compared with their environmental habitat. This suggests that although pre- and post-metamorphic toad life stages differ from each other, the habitat and host fungal communities are so similar that identifying obligate host symbionts is difficult with the techniques used here. This approach does, however, leverage sequence data from host and habitat samples to predict which microbial taxa are host-associated versus transient microbes, thereby condensing a large set of sequence data into a smaller list of potential targets for further consideration. DOI
2. Lemay, MA; Chen, MLY; Mazel, F; Hind, KR; Starko, S; Keeling, PJ; Martone, PT; Parfrey, LW. (2021) Morphological complexity affects the diversity of marine microbiomes.ISME J. 15: 1372-1386 Morphological complexity affects the diversity of marine microbiomes
Large eukaryotes support diverse communities of microbes on their surface-epibiota-that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity-host evolutionary history and ecology, environmental conditions and stochasticity-do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities. DOI
1.Chen, MY; Parfrey, LW. (2018) Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae.Mol. Ecol. 27: 1966-1979 Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae
16S rRNA; community assembly; Mastocarpus; microbial ecology; Nereocystis; seaweed
Macroalgae variably promote and deter microbial growth through release of organic carbon and antimicrobial compounds into the water column. Consequently, macroalgae influence the microbial composition of the surrounding water column and biofilms on nearby surfaces. Here, we use manipulative experiments to test the hypotheses that (i) Nereocystis luetkeana and Mastocarpus sp. macroalgae alter the water column microbiota in species-specific manner, that (ii) neighbouring macroalgae alter the bacterial communities on the surface (epibiota) of actively growing Nereocystis luetkeana meristem fragments (NMFs), and that (iii) neighbours alter NMF growth rate. We also assess the impact of laboratory incubation on macroalgal epibiota by comparing each species to wild counterparts. We find strong differences between the Nereocystis and Mastocarpus epibiota that are maintained in the laboratory. Nereocystis and Mastocarpus alter water column bacterial community composition and richness in a species specific manner, but cause only small compositional shifts on NMF surfaces that do not differ by species, and do not change richness. Co-incubation with macroalgae results in significant change in abundance of fivefold more genera in the water column compared to NMF surfaces, although the direction (i.e., enrichment or reduction) of shift is generally consistent between the water and NMF surfaces. Finally, NMFs grew during the experiment, but growth did not depend on the presence or identity of neighbouring macroalgae. Thus, macroalgae exhibit a strong and species-specific influence on the water column microbiota, but a much weaker influence on the epibiota of neighbouring macroalgae. Overall, these results support the idea that macroalgae surfaces are highly selective and demonstrate that modulations of macroalgal microbiota operate within an overarching paradigm of host species specificity. DOI
