Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

The intersection of genotype and phenotype to inform ecotype development (#181)

Bhavya Nalagampalli Papudeshi 1 , Thiago Bruce 2 , Rebecca deWardt 3 , Blaire Robinson 3 , Daniel A Cuevas 4 , Kristen Aguinaldo 3 , Tucker Lopez 3 , Maria F Mora 3 , Katelyn McNair 4 , Meredith Peterson 3 , Abigail C Turnland 5 , Dominic Cavalli 3 , Matthew J Haggerty 3 , Ashani Kumudika Susinghe 3 , Robert A Edwards 1 , Elizabeth A Dinsdale 1
  1. Flinders University, Adelaide, SA, Australia
  2. Microbiology Department, Universidade Federal da Bahia, Salvador, Bahia, Brasil
  3. Biology Department, San Diego State University, San Diego, California, USA
  4. Computational Science Research Center, San Diego State University, San Diego, California, United States
  5. Australian Center for Ecogenomics, The University of Queensland, St Lucia, St Lucia, Queensland, Australia

Genotype to phenotype associations are fundamental to biology. Genetic traits are continuously molded through gene gain or loss of functions to best adapt to the local environment that are then reflected as phenotypic traits. Here we investigate the emergence of new ecotypes that result from decoupling of functional variation from taxonomic variation among nine Vibrio species isolated from either the surface of the giant kelp, Macrocystis pyrifera, or water from the kelp forest off the southern California coast. The isolates were sequenced on Illumina MiSeq and Nanopore MinION platforms, and two circular chromosomes were assembled for all isolates. We compared each isolates ability to utilize 71 carbon substrates using microarrays. Clustering based on genomic and phenotypic profiles showed that environment was not correlated to genotype or phenotype, and genotype did not cluster with phenotype. 

We focused on genetically similar isolates: kelp-associated Vibrio spp. ED008 and water-associated with Vibrio spp. ED582 share 97.73% ANI but have distinct phenotypic profiles growing on 6 and 22 substrates respectively. Genotype to phenotype association was performed through a genomic comparison after reconstructing the metabolic models from functions and gap-filling based on their phenotype using PyFBA. This analysis identified genetic differences explaining 11 phenotypic differences. For instance, ED008 was able to utilize glucose-6-phosphate (Glc6P) due to the presence of hexose phosphate transport system that allows the substrate to enter the cell. Transcriptome analysis demonstrated that this transport system was significantly upregulated (p < 0.01, and < 2 fold coverage) in Glc6P compared to control. 

The differences reflect the ecological differentiation adapted by these isolates to survive in different environments. ED008 is a specialist utilizing specific carbon sources available on the kelp surface, whereas ED582 is a  generalist that can utilize a range of carbon sources due to the sparse availability of nutrients in the water. Our findings demonstrate the genetic basis of ecotype development through mapping genotype to phenotypes.