Proteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnology

Abstract

Summary Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications.

Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration

“…Part of the harvested biomass was immediately frozen at -80 Following the 2 years of cultivation in tubular PBRs, biomass grown in "high-pH nitrate" medium showed the highest growth rate and was transferred to a set of stirred 10 L glass bottle PBRs with "high-pH nitrate" medium (Supplementary Figure 14B). These PBRs were stirred at 300-330 RPM as previously described (Ataeian et al, 2021). In these systems, the biomass grew as small biomass aggregates that rapidly co-aggulated during harvesting, after the stirrer was stopped.…”

“…Shotgun metagenomic sequencing (2 × 300 bp) was performed using an Illumina MiSeq sequencer. Read quality control and assembly was performed as described in Ataeian et al (2021).…”

“…Previously, we enriched a cyanobacterial consortium in laboratory photobioreactors (PBRs) (Ataeian et al, 2019) from microbial mats of four alkaline soda lakes located on Cariboo Plateau, BC, Canada (Brady et al, 2013;Zorz et al, 2019). Recently, we introduced Candidatus "Phormidium alkaliphilum, " the most abundant member and the only cyanobacterium in the consortium (Ataeian et al, 2021). Here, we focus on the roles of the heterotrophic members of the consortium.…”

“…Here, we focus on the roles of the heterotrophic members of the consortium. For this, we made use of five metagenomes, collected from different cultures and time points as previously described (Ataeian et al, 2021). Two cultures had an initial pH of 8.3 (low-pH), one received ammonium as the nitrogen source, the other nitrate.…”

“…Although each lake has a different microbial community structure, a nearly identical cyanobacterial consortium was enriched from each lake in laboratory photobioreactors (PBRs) (Sharp et al, 2017). More than 80% of the consortium consisted of a Candidatus Phormidium alkaliphilum (Ataeian et al, 2021) maintaining a high and robust biomass productivity of 15.2 ± 1.0 g/m 2 /day (Ataeian et al, 2019) during 4 years of crash-free growth in open laboratory culture.…”