Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes

Abstract

Morphological plasticity is a genotype-by-environment interaction that enables organisms to increase fitness across varying environments. Symbioses with diverse microbiota may aid in acclimating to this variation, but whether the associated bacteria community is phenotype specific remains understudied. Here we induce morphological plasticity in three species of sea urchin larvae and measure changes in the associated bacterial community. While each host species has unique bacterial communities, the expression of plasticity results in the convergence on a phenotype-specific microbiome that is, in part, driven by differential association with α- and γ-proteobacteria. Furthermore, these results suggest that phenotype-specific signatures are the product of the environment and are correlated with ingestive and digestive structures. By manipulating diet quantity over time, we also show that differentially associating with microbiota along a phenotypic continuum is bidirectional. Taken together, our data support the idea of a phenotype-specific microbial community and that phenotypic plasticity extends beyond a genotype-by-environment interaction.

Bacterial Exposure Mediates Developmental Plasticity and Resistance to Lethal Vibrio lentus Infection in Purple Sea Urchin (Strongylocentrotus purpuratus) Larvae

“…Laboratory (AEW)-and natural seawater (NSW)-exposed larvae raised for comparison by 16S rRNA sequencing were cultured as above but collected somewhat differently, reflecting standard practices used by inland and field-based laboratories in previous studies [e.g., (22) vs. (28,38)]. Laboratory-reared larvae were raised in AEW but washed to remove unassociated microorganisms and flocculent debris prior to sample processing (see below).…”

“…These animals were then starved at ∼2-5 larvae/mL in 0.2 µm-filtered FSW overnight prior to sample processing to minimize the contribution from microorganisms that were only transiently present in the gut lumen. NSW-raised larvae were collected directly by centrifugation and seawater removal (28). In all cases, treatment-matched Rhodomonas samples were spun down at 800 g for 3 min, washed in FSW, and similarly processed.…”

“…Using QIIME 1.9.1 [or Quantitative Insights Into Microbial Ecology; (59)], bacterial 16S rRNA sequences were analyzed and grouped into operational taxonomic units (OTUs) based on a minimum 97% similarity. The biom table generated by the pick_open_reference_otus.py script was filtered of OTUs with 10 or fewer reads as well as sequences matching the chloroplasts of cryptophytes [i.e., R. lens; (28)].…”

“…Associated bacteria have been characterized in diverse echinoderm taxa at many stages of development (22,(26)(27)(28)(29)(30)(31), but spatiotemporal colonization kinetics in sea urchin larva remain poorly described (19,69). Two likely sites for bacterial colonization are the larval digestive tract and the ectoderm, whether its external surface or the subcuticular space (70,71).…”

“…Ilya Metchnikoff first described cellular immunity in echinoderm larvae in the late 1800s (20), and recently, researchers have returned to these organisms with modern genomic, experimental, and imaging techniques, describing the specialized immune cell types of echinoderm larvae and their functions in response to diverse challenges [e.g., (21)(22)(23)(24); reviewed in (17,19,25)]. In parallel, embryonic, larval, and adult echinoderm bacterial microbiomes have been characterized in several species [e.g., (22,(26)(27)(28)(29)(30)(31); reviewed in (19)]. These studies focused on bacteria acquired in natural seawater or in the wild, but major questions that remain are to what degree artificial seawater-raised laboratory animals recapitulate the microbiota of their wild counterparts (32,33) and how these differences Abbreviations: FSW, artificial filtered seawater; P/S, 0.2 µm-filtered artificial seawater + 100 U/mL penicillin, 100 µg/mL streptomycin; AEW, artificial filtered seawater + 20% (v/v) adult-exposed tank water; CFU, colony-forming unit; dpf, days post fertilization; NSW, natural seawater; hpf, hours post fertilization; OTU, operational taxonomic unit; PCoA, principle coordinate analysis.…”