UC San Diego

Cyanobacterial biofilms are not only important as critical components of ecological habitats, but have applications in wastewater treatment systems, bioremediation efforts, and prevention of biofouling. Strains of the freshwater cyanobacterium Synechococcus elongatus were first isolated approximately 60 years ago, and PCC 7942 is well established as a model for photosynthesis, circadian biology, and biotechnology research. PCC 7942 is planktonic in lab conditions, but studies of biofilming mutants support a model of constitutive repression of biofilms in PCC 7942. A recent environmental isolate of S. elongatus, UTEX 3055, shares 98.46% average nucleotide identity with PCC 7942, but has unique phenotypes of phototaxis and robust biofilm formation in laboratory conditions. This genetic similarity and the constitutive repression of biofilm formation suggests that lab strains of S. elongatus may be domesticated. An approach combining comparative genomics analysis with the use of random barcoded transposon sequencing (RB-TnSeq) library screens was used to find the genetic basis of biofilm and phototaxis phenotypes in S. elongatus. This work describes the sequencing and annotation of UTEX 3055 as well as the characterization of a novel phototaxis operon in the strain; a comprehensive genome comparison of S. elongatus strains that provides a pangenome annotation, a corrected sequence for the type strain PCC 6301, and identification of genes controlling pigmentation and phototaxis phenotypes; the creation of an RB-TnSeq library in UTEX 3055 that can be used in future fitness screening experiments; and an IRB-Seq experiment in PCC 7942 that provides genetic targets to expand the current model of biofilm formation in S. elongatus.