The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Moritz Koch; Avery J C Noonan; Yilin Qiu; Kalen Dofher; Brandon Kieft; Soheyl Mottahedeh; Manisha Shastri; Steven J Hallam

doi:10.3389/fbioe.2022.932695

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Front Bioeng Biotechnol. 2022 Aug 15:10:932695. doi: 10.3389/fbioe.2022.932695. eCollection 2022.

Authors

Moritz Koch¹, Avery J C Noonan^{2

3}, Yilin Qiu², Kalen Dofher², Brandon Kieft¹, Soheyl Mottahedeh⁴, Manisha Shastri⁴, Steven J Hallam^{1

2

3

5

6}

Affiliations

¹ Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
² Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada.
³ ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada.
⁴ AlgaBloom International Ltd., Richmond, BC, Canada.
⁵ Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
⁶ Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.

Abstract

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

Keywords: cyanobacteria; isolate; oscillatoriales; phormidium; photobioreactor; stress tolerance.

Grants and funding

This work was performed under the auspices of the Natural Sciences and Engineering Research Council (NSERC) of Canada, Genome British Columbia, the Canada Foundation for Innovation (CFI). The US Department of Energy (DOE) Joint Genome Institute (JGI) and the Facilities Integrating Collaborations for User Science (FICUS) JGI-EMSL (Environmental Molecular Science Laboratory) project (10.46936/fics.proj. 2019.50967/60000128) supported by the Office of Science of US DOE Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL), and the G. Unger Vetlesen and Ambrose Monell Foundations with essential automation support through the Biofactorial automation core facility in the Life Sciences Institute at the University of British Columbia. AN was supported by the NSERC CREATE Ecosystem Services, Commercialization Platforms and Entrepreneurship (ECOSCOPE) training program at the University of British Columbia and the Mitacs Global Link program. YQ, AN, and KD were also supported by the NSERC CREATE Genome Sciences and Technology (GSAT) training program at the University of British Columbia.