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1. Host genotype structures the microbiome of a globally dispersed marine phytoplankton

   https://doi.org/10.1073/pnas.2105207118  

   Ahern, Olivia M.; Whittaker, Kerry A.; Williams, Tiffany C.; Hunt, Dana E.; Rynearson, Tatiana A. (November 2021, Proceedings of the National Academy of Sciences)

   Phytoplankton support complex bacterial microbiomes that rely on phytoplankton-derived extracellular compounds and perform functions necessary for algal growth. Recent work has revealed sophisticated interactions and exchanges of molecules between specific phytoplankton–bacteria pairs, but the role of host genotype in regulating those interactions is unknown. Here, we show how phytoplankton microbiomes are shaped by intraspecific genetic variation in the host using global environmental isolates of the model phytoplankton host Thalassiosira rotula and a laboratory common garden experiment. A set of 81 environmental T. rotula genotypes from three ocean basins and eight genetically distinct populations did not reveal a core microbiome. While no single bacterial phylotype was shared across all genotypes, we found strong genotypic influence of T. rotula , with microbiomes associating more strongly with host genetic population than with environmental factors. The microbiome association with host genetic population persisted across different ocean basins, suggesting that microbiomes may be associated with host populations for decades. To isolate the impact of host genotype on microbiomes, a common garden experiment using eight genotypes from three distinct host populations again found that host genotype influenced microbial community composition, suggesting that a process we describe as genotypic filtering, analogous to environmental filtering, shapes phytoplankton microbiomes. In both the environmental and laboratory studies, microbiome variation between genotypes suggests that other factors influenced microbiome composition but did not swamp the dominant signal of host genetic background. The long-term association of microbiomes with specific host genotypes reveals a possible mechanism explaining the evolution and maintenance of complex phytoplankton–bacteria chemical exchanges. 

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2. Mobile genetic elements exhibit associated patterns of host range variation and sequence diversity within the gut microbiome of the European Honey bee

   https://doi.org/10.1101/2025.01.31.635958  

   Robinson, Chris_R P; Dolezal, Adam G; Liachko, Ivan; Newton, Irene_L G (February 2025, bioRxiv)

   Abstract Mobile genetic elements (MGEs), such as plasmids and bacteriophages, are major contributors to the ecology and evolution of host-associated microbes due to a continuum of symbiotic interactions and by mediating gene flow via horizontal gene transmission. However, while myriad studies have investigated relationships between MGEs and variation in fitness among microbial and eukaryotic hosts, few studies have incorporated this variation into the context of MGE evolution and ecology. Combining HiC-resolved metagenomics with the model honey bee worker gut microbiome, we show that the worker gut contains a dense, nested MGE community that exhibits a wide degree of host range variation among microbial hosts. Using measures of gene similarity and syntenty, we show that plasmids likely mediate gene flow between individual honey bee colonies, though these plasmids exhibit broad host range variation within their individual microbiomes. We further show that phage-microbe networks exhibit high variation among individual metagenomes, and that phages show broad host range with respect to both the number and phylogenetic distance of their hosts. Finally, we provide evidence that measures of nucleotide variation positively correlate with host range in bee-associated phages, and that functional targets of diversifying selection are partitioning differently between broad or narrow host range phages. Our work underscores the variability of MGE x microbial interactions within host-associated microbial communities and highlights the genomic variation associated with MGE host range diversity. 

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3. Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals

   https://doi.org/10.3390/microorganisms9091873  

   Messyasz, Adriana; Maher, Rebecca L.; Meiling, Sonora S.; Thurber, Rebecca Vega (September 2021, Microorganisms)

   null (Ed.)

   While studies show that nutrient pollution shifts reef trophic interactions between fish, macroalgae, and corals, we know less about how the microbiomes associated with these organisms react to such disturbances. To investigate how microbiome dynamics are affected during nutrient pollution, we exposed replicate Porites lobata corals colonized by the fish Stegastes nigricans, which farm an algal matrix on the coral, to a pulse of nutrient enrichment over a two-month period and examined the microbiome of each partner using 16S amplicon analysis. We found 51 amplicon sequence variants (ASVs) shared among the three hosts. Coral microbiomes had the lowest diversity with over 98% of the microbiome dominated by a single genus, Endozoicomonas. Fish and algal matrix microbiomes were ~20 to 70× more diverse and had higher evenness compared to the corals. The addition of nutrients significantly increased species richness and community variability between samples of coral microbiomes but not the fish or algal matrix microbiomes, demonstrating that coral microbiomes are less resistant to nutrient pollution than their trophic partners. Furthermore, the 51 common ASVs within the 3 hosts indicate microbes that may be shared or transmitted between these closely associated organisms, including Vibrionaceae bacteria, many of which can be pathogenic to corals. 

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4. Pathogen-microbiome interactions and the virulence of an entomopathogenic fungus

   https://doi.org/10.1128/aem.02293-23  

   Kolp, Matthew R; de_Anda_Acosta, Yazmin; Brewer, William; Nichols, Holly L; Goldstein, Elliott B; Tallapragada, Keertana; Parker, Benjamin J (June 2024, Applied and Environmental Microbiology)

   Tortosa, Pablo (Ed.)

   ABSTRACT Bacteria shape interactions between hosts and fungal pathogens. In some cases, bacteria associated with fungi are essential for pathogen virulence. In other systems, host-associated microbiomes confer resistance against fungal pathogens. We studied an aphid-specific entomopathogenic fungus calledPandora neoaphidisin the context of both host and pathogen microbiomes. Aphids host several species of heritable bacteria, some of which confer resistance againstPandora. We first found that spores that emerged from aphids that harbored protective bacteria were less virulent against subsequent hosts and did not grow on plate media. We then used 16S amplicon sequencing to study the bacterial microbiome of fungal mycelia and spores during plate culturing and host infection. We found that the bacterial community is remarkably stable in culture despite dramatic changes in pathogen virulence. Last, we used an experimentally transformed symbiont of aphids to show thatPandoracan acquire host-associated bacteria during infection. Our results uncover new roles for bacteria in the dynamics of aphid-pathogen interactions and illustrate the importance of the broader microbiological context in studies of fungal pathogenesis. IMPORTANCEEntomopathogenic fungi play important roles in the population dynamics of many insect species. Understanding the factors shaping entomopathogen virulence is critical for agricultural management and for the use of fungi in pest biocontrol. We show that heritable bacteria in aphids, which confer protection to their hosts against fungal entomopathogens, influence virulence against subsequent hosts. Aphids reproduce asexually and are typically surrounded by genetically identical offspring, and thus these effects likely shape the dynamics of fungal disease in aphid populations. Furthermore, fungal entomopathogens are known to rapidly lose virulence in lab culture, complicating their laboratory use. We show that this phenomenon is not driven by changes in the associated bacterial microbiome. These results contribute to our broader understanding of the aphid model system and shed light on the biology of the Entomophthorales—an important but understudied group of fungi. 

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5. Metabarcoding Approaches in Amphibian Disease Ecology: Disentangling the Functional Contributions of Skin Bacteria on Disease Outcome

   https://doi.org/10.1093/icb/icac062  

   Longo, Ana V (May 2022, Integrative and Comparative Biology)

   Abstract Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host–pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I reanalyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems. 

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