Description of a novel extremophile green algae, Chlamydomonas pacifica, and its potential as a biotechnology host
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Abstract
We present the comprehensive characterization of a newly identified microalga, Chlamydomonas pacifica, originally isolated from a soil sample in San Diego, CA, USA. This species showcases remarkable biological versatility, including a broad pH range tolerance (6-11.5), high thermal tolerance (up to 42 degree celsius), and salinity resilience (up to 2% NaCl). Its amenability to genetic manipulation and sexual reproduction via mating, particularly between the two opposing strains CC-5697 & CC-5699, now publicly available through the Chlamydomonas Resource Center, underscores its potential as a biotechnological chassis. The biological assessment of C. pacifica revealed versatile metabolic capabilities, including diverse nitrogen assimilation capability, motility and phototaxis. Genomic and transcriptomic analyses identified 17,829 genes within a 121 Mb genome, featuring a GC content of 61%. The codon usage of C. pacifica closely mirrors that of C. reinhardtii, indicating a conserved genetic architecture that supports a trend in codon preference with minor variations. Phylogenetic analyses position C. pacifica within the core-Reinhardtinia clade yet distinct from known Volvocales species. The lipidomic data revealed an abundance of triacylglycerols (TAGs), promising for biofuel applications and lipids for health-related benefits. Our investigation lays the groundwork for exploiting C. pacifica in biotechnological applications, from biofuel generation to synthesizing biodegradable plastics, positioning it as a versatile host for future bioengineering endeavors.
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It can be, and I will add in the next version. For now, here is one short clip with the overlayed tracks.
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Thank you, Ryan. Shortly, no. I will add a more in-depth description in the next version. However, we were concerned about the conclusions drawn from the video and kept within what was possible. As you point out, cells move in three dimensions in the assay. This affects the conclusion of population speed information. I will point it out in the manuscript so readers can observe the graphs to estimate the speed and be aware of the three-dimensional effects of observed speed. Any individual speed observed is also affected by cells swimming non-perpendicular to the camera point. A better chamber device might help access it better in the future. From the graph, I would expect the max speed to be close to the actual value since no spatial effect would artificially increase it.
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A neutral white light (a fluorescent bulb, model UCL 7000-1) was used next to the plate. I'm curious about motility behavior and I wonder if it is related to intensity. I will add this information in the next version.
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I believe it could differentiate even further from C. reinhardtii or other Chlamydomonas, and I would like to test it if possible. Regarding the change in speed, the underlying mechanism would probably be a combination of factors requiring well-placed controls to sort. Salinity probably affects cytoplasmatic membrane functions, and flagella movement is controlled there in C. reinhardtii.
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We have kept them in staving conditions for 10-20 minutes. Previously, working with C. reinhardtii, I had similar timelines. However, I did notice that sub-culturing in liquid to much reduced motility or recovery of motility. I have not pinpointed the actual cause, but I had the impression that starting from agar plates was better, at least for gametogenesis and mating. I started doing that for C. reinhardtii after reading (https://en.bio-protocol.org/pdf/Bio-protocol4705.pdf)
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All supplemental materials are also included in the figshare link.
I'm curious if your light microscopy data used for cell tracking is, or could also be, made available?
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the recorded video was analyzed with ImageJ’s plugin TrackMate (6.01)
Cool video! I'm curious though if any filtering of the trajectories was done to prevent individual cells from being counted multiple times in the statistics? Relatively faster cells that dip in and out of focus, for instance, could skew the speed distribution if not taken into consideration.
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The cells were observed with a Nikon microscope equipped with a Nikon DS-Qi2 camera
What light source was used and what was the duration of the videos for the motility assay? Given their negative phototaxis, I'm wondering if red light was used for imaging.
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The ability to move strategically allows these algae to seek desirable niches for growth and survival, especially in extreme habitats where resources are scarce or conditions are rapidly changing.
Is C. pacifica's capacity to live in higher salinity environments accompanied by variation in their motility patterns with respect to non-extremophiles? Given that the Reynold's number varies with salinity, it might be enlightening to measure C. pacifica's speed distribution at different salinity concentrations. I wonder if these experiments might uncover more interesting axes of diversity within C. pacifica that differentiate them from species like C. reinhardtii.
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resuspended in nitrogen-free HSM media to trigger gametogenesis and enhance flagellar movement.
How long were the cells incubated in the nitrogen-free HSM medium before the phototaxis and motility assays? We've observed variation in gametic motility depending on the time spent in water prior to the assay.
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