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

In search of the pH limit of growth in halo-alkaliphilic cyanobacteria

Cyanobacteria have many biotechnological applications. Increasing their cultivation pH can assist in capturing carbon dioxide and avoiding invasion by other organisms. However, alkaline media may have adverse effects on cyanobacteria, such as reducing the Carbon-Concentrating Mechanism's efficiency. Here, we cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.

Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium

Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.

Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment

We report the genome of Phormidium yuhuli AB48, which includes a circular chromosome and a circular plasmid (4,747,469 bp and 51,599 bp, respectively). This is currently the only closed reference genome of an isolate of the Phormidium genus, based on the Genome Taxonomy Database (GTDB), providing a potential model system for sustainable biotechnology innovation.

Metagenome-Assembled Genomes for “ Candidatus Phormidium sp. Strain AB48” and Co-occurring Microorganisms from an Industrial Photobioreactor Environment

Here, we report metagenome-assembled genomes for “ Candidatus Phormidium sp. strain AB48” and three cooccurring microorganisms from a biofilm-forming industrial photobioreactor environment, using the PacBio sequencing platform. Several mobile genetic elements, including a double-stranded DNA phage and plasmids, were also recovered, with the potential to mediate gene transfer within the biofilm community.

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

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].

Nutrient management and medium reuse for cultivation of a cyanobacterial consortium at high pH and alkalinity

Alkaliphilic cyanobacteria have gained significant interest due to their robustness, high productivity, and ability to convert CO2 into bioenergy and other high value products. Effective nutrient management, such as re-use of spent medium, will be essential to realize sustainable applications with minimal environmental impacts. In this study, we determined the solubility and uptake of nutrients by an alkaliphilic cyanobacterial consortium grown at high pH and alkalinity. Except for Mg, Ca, Co, and Fe, all nutrients are in fully soluble form. The cyanobacterial consortium grew well without any inhibition and an overall productivity of 0.15 g L−1 d−1 (AFDW) was achieved. Quantification of nutrient uptake during growth resulted in the empirical formula CH1.81N0.17O0.20P0.013S0.009 for the consortium biomass. We showed that spent medium can be reused for at least five growth/harvest cycles. After an adaptation period, the cyanobacterial consortium fully acclimatized to the spent medium, resulting in complete restoration of biomass productivity.

Pilot-scale outdoor trial of a cyanobacterial consortium at pH 11 in a photobioreactor at high latitude

The biomass of microalgae and cyanobacteria yields a variety of products. Outdoor pilot plant trials typically grow a single species at circumneutral pH and provide CO₂ by gas sparging. Here a cyanobacterial consortium was grown at high pH (beyond 11) and high dissolved carbonate concentrations (0.5 M) in an outdoor 1,150 L tubular photobioreactor for 130 days in Calgary, Canada. The aim was to assess the productivity and robustness of the consortium. Importantly, the system was designed to enable future integration of air capture of CO₂. Productivity was between 3.1 and 5.8 g ash-free dry weight per square metre per day, depending on biomass density and month. 16S rRNA amplicon sequencing showed that cyanobacterium Candidatus "Phormidium alkaliphilum" made up 80% of the consortium. The consortium displayed robust growth and adapted to environmental conditions. Bicarbonate uptake pushed medium pH past 11, demonstrating the ability to achieve CO₂ delivery by air capture.

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

Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.