Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater

Abstract

Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp . Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 > 2 Mb and genomic completeness ≥91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a ~1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum , which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.

Multiomics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

“…[ 187 ] Comparative genomic analysis of a Chlorella strain that shows best WWT ability with other two strains provides fundamental information to unveil the molecular basis of abiotic stress tolerance in WWT, which is essential for future genetic engineering of strain suitable for swine WWT. [ 188,192 ] Moreover, the nutrient removal and biomass accumulation efficiency of microalgae can be increased by genetic modifications in cellular pathways by gene transformations and new genome‐editing techniques that are nuclear, chloroplast, and mitochondrial genomes based for up‐ or downregulation of the crucial steps of target metabolism(s) through selection approaches for targeting specific gene modification. [ 189 ] Gene‐editing technology such as CRISPR/Cas9 system has been successfully developed in several microalgae frequently applied in WWT, for example, D .…”

Wastewater treatment by microalgae

“…cells were able to achieve a removal of 90% of not only phosphate, but also ammonium and nitrate from synthetic wastewater (Shi et al, 2007 (Wang et al, 2010). Overall, Chlorella is one the most commonly used genus of microalgae for wastewater treatment as it can adapt well to many types of wastewaters and is extremely efficient at removing a variety of pollutants (Wu et al, 2019).…”

“…was able to remove up to 100% of Fe 2+ and Mn 2+ , 70–87% of Al 3+ , and 80–98% of Mg 2+ from four different types of wastewater (Wang et al, 2010). Overall, Chlorella is one the most commonly used genus of microalgae for wastewater treatment as it can adapt well to many types of wastewaters and is extremely efficient at removing a variety of pollutants (Wu et al, 2019).…”

Grand Challenges in Microalgae Domestication

“…Chlorella are maintained in haploid form, and it is difficult to know whether sexual reproduction could be obtained. Genomic data have been made available recently for a few strains (Wu et al, 2019 ) and transformation mediated by Agrobacterium tumefaciens is possible (Cha et al, 2012 ; Sharma et al, 2021 ). Dunalliella has a main haploid cycle, but sexual reproduction is known.…”