June 29, 2020 | Margaret Helder

Diatoms Defy the Evolutionary Endosymbiosis Theory

Why Endosymbiosis Cannot Explain Diatoms –
Or Anything Else

By Margaret Helder, PhD

Diatoms: Talent Content Winners

Diatom photos by Mark Armitage.

To the people most familiar with them, algae are not only beautiful, but also highly diverse in their appearance, physiology and ecology. There are many remarkable taxa with claims to these flattering descriptions, but perhaps the diatoms are the ultimate in each of these categories. As far as beauty is concerned, the glass walls of these cells, so precisely marked with pores and raised areas and spines, most certainly claim the prize. As far as diversity of habitats goes, the diatoms are tops there too. They are important components of the phytoplankton in both marine and freshwater habitats. They also grow on underwater surfaces such as aquatic plants. Some specialists estimate that diatoms carry out about 45% of global primary production as a result of their rapid rate of cell division.1

One of the main reasons for the ecological success of the diatoms is their photosynthetic apparatus which is localized in golden colored plastids [or chloroplasts]. As a result of unique light harvesting strategies, these cells are able to exploit a broad spectrum of light quality in their watery habitats and this leads to their spectacular success as primary producers [producing food for all the consumers higher up the food chain].

Photosynthesis: their best talent

A recent article in Nature Communications focuses on a most important area of diatom physiology, the harvesting of light energy to drive photosynthesis.2 Inside the chloroplast, there are two different photosystems, each a large complex of different proteins and pigments that is optimized to harvest light. Whereas photosystem II provides energy for the water splitting and oxygen releasing process, photosystem I provides energy to reduce carbon dioxide to organic compounds like sugar. [Sugar provides food energy whereas carbon dioxide does not.] All aerobic photosynthetic organisms possess such photosystems, but the details vary and thus the efficacy of the photosynthesizing organism varies with environmental conditions.

The recent article focuses on the photosystem I light-harvesting complex in a marine diatom. The performance of a given photosystem depends on the component parts of the core and surrounding proteins which are shaped so as to attract connections with specific important pigments. Assuming that red algae and green algae represent the most basic designs of photosynthetic organization, a study of this diatom reveals that its system is different.

Upon investigation of the photosystem I core, the scientific team discovered that the diatom model displayed some unique aspects when compared to other aerobic autotrophs (photosynthesizers)3. While there are ten subunits in diatoms which are found in common with other taxa, there are four that are missing. Of these, one is found in all other aerobic autotrophs, two are found only in green algae and land plants, and one is found in all aerobic autotrophs except cyanobacteria (blue green algae). These are significant omissions. Also there are two totally unique subunits in the photosystem I core.4 How did these originate?

But that is not all that is unique about the photosystem I supercomplex. The number of associated proteins, for a start, is highly unusual. The diatoms exhibit 16 encircling subunits (eleven more than red or green autotrophs) and of these, six are classified as a unique type of protein whose function is unknown. Since diatoms are so unusually successful as primary producers (photosynthesizers), it seems fair to conclude that these observed differences contribute to their success. Thus, the authors conclude:

“the increased number of light-harvesting complex subunits in diatoms confer them with special capabilities of light-harvesting and energy quenching under the aquatic environment conditions, where light is often limited and its intensity is highly fluctuated.”5

However, if there is one thing that many biologists do not like, it is unique features in living creatures which are difficult to explain in an evolutionary context. This brings our attention to the reigning evolutionary explanation which endeavors to explain how functional unique features could spontaneously appear.

Where did these talents come from?

Diatoms, according to explanations involving ‘endosymbiosis’ are at the tail end of a long and complicated process. The original endosymbiotic event occurred, so the popular understanding goes, when a eukaryotic heterotrophic cell engulfed a free living photosynthetic cyanobacterium. [Note: a eukaryotic cell has a nucleus; a heterotroph is dependent on other sources of nutrients, as opposed to an autotroph, which makes its own nutrients.] The victim did not possess a membrane-bound nucleus, the story goes, but it was capable of photosynthesizing. For unknown reasons, the hungry host cell apparently did not digest the victim cell, as would normally be expected, but retained it as a “hostage”. Accordingly, the host thus benefited from the products of photosynthesis that the hostage provided. This is the simplistic tale of endosymbiosis. Things get a lot messier in the details.

The pigments in the blue-green hostage are chemically related to red pigments in red seaweeds. The theory proposes that these primary pigments in some cells changed into the very different green algal pigments. That’s easier said than done. One long-time expert in the field, John Archibald declared in a review article that “the technical and conceptual challenges associated with inferring such ancient evolutionary events are considerable.” 6

Oversimplified diagram of endosymbiosis

Moving genes and inventing proteins

Engulfing and retaining an ‘endosymbiont’ are the ‘easy’ parts of the process. Since in every eukaryotic autotroph, most of the genes which control the activities of the ‘hostage’ are in fact found inside the host nucleus, biologists have to assume that “intracellular (or endosymbiotic) gene transfer (EGT) was a major factor in the integration of the cyanobacterial progenitor of the plastid and its eukaryotic host.” 7 How exactly genes were able to move from the hostage into the central nucleus to become incorporated into the chromosomes there, is anybody’s guess. But again, that was the ‘easy’ part of the process. Since the genes in the nucleus control protein synthesis in the cytoplasm, not in the chloroplast, [but since those proteins have to function inside the chloroplast], new, dedicated proteins also have to appear to facilitate transport of these proteins into the chloroplast. Where did the newly required (and highly specific) transport proteins come from?

But on the way to diatoms, the above is the ‘easy’ part of the process. If you thought one endosymbiotic event was fraught with hazards, how about five? The really tricky event is a secondary event, or a tertiary event, or more. The scenario goes like this. A heterotrophic eukaryote (as before) engulfs a whole eukaryotic photosynthetic cell (not as before – this time the engulfed cell has a nucleus and a contained plastid). So now we have a host cell with a hostage inside that includes a nucleus and chloroplast. As per what we saw before, inside the hostage cell, many of the genes from the chloroplast have moved into the nucleus. Now these genes in the hostage nucleus move to the host nucleus and also some of the genes from the hostage chloroplast also move into the host cell nucleus. In the end, all that remains of the hostage is the chloroplast. Its nucleus and other cell structures have all disappeared – at least they are presumed to have been lost, as they are not there.8

Diatoms (Mark Armitage)

Back to the diatoms. They are presumed to be the beneficiaries of several endosymbiotic events. Our story starts with the primary endosymbiotic event in which a hungry eukaryote engulfed a cyanobacterium, resulting in a red alga. A paper in 2017, however, suggested that a further endosymbiotic event was required within the red algae to explain the diversity found within the photosynthetic genes in the reds.9 So we will call this a ‘cryptic’ [hidden] endosymbiotic event. So far two endosymbiotic events have been proposed.

We now proceed on to a possible endosymbiotic event involving the engulfing of a green alga. Several studies have suggested that important photosynthetic genes in the diatom nucleus include a large number which are characteristic of green algae. Moustafa et al. (2009) call the diatom  nuclear genes “highly chimeric” or a blend from disparate sources.10 Thus Benoiston (2017) declares:

“the abundance of genes apparently derived from a green algal source has led to the controversial hypothesis that a green algal endosymbiont preceded the red alga and that many of its [green] genes were retained prior to the arrival of the red alga whereas the red algal genes that were acquired later were not [retained].” 11

The upshot of this cryptic event, says Benoiston was that, “In such a scenario, diatoms (and other photosynthetic chromalveolates) bear red-algal derived chloroplasts driven to a significant extent by green algal genes encoded in the nucleus.”12 Others who support such an idea include Chan et al. who declare ,“Given that the red algal secondary endosymbiosis occurred > 1 billion years ago, the putative green algal endosymbiosis must have occurred earlier.”13  Both Chan et al. and Benoiston et al. consider that this cryptic endosymbiotic event may have conferred significant advantages on descendants such as the diatoms.14 Other authors however such as Deschamps and Moreira (2012) discourage any conclusions about a cryptic green symbiosis.15

At last we get to the secondary endosymbiosis event involving a eukaryote with green photosynthetic genes in its nucleus which engulfs a cell with a red chloroplast. Of this event, Archibold declares:

“One of the most intriguing aspects of secondary and tertiary endosymbiosis is the fate of the endosymbiont [hostage] nucleus and the essential genes it harbors. Most secondary- and tertiary-plastid-containing organisms have completely done away with the primary algal nucleus that accompanied the plastid. Consequently, the hundreds of plastid genes that moved from the original cyanobacterial endosymbiont to the host nucleus during primary endosymbiosis must have moved again, this time from the primary host nucleus to that of the secondary host.”16

And for diatoms, some experts imagine that a tertiary endosymbiosis occurred with all this moving of genes again!17 The end result of this highly imaginary series of events is like a miracle:

“The chimeric nature of diatom genomes has brought together unique combinations of genes that collectively encode non-canonical pathways of nutrient assimilation and metabolic management.”18

Explanatory choices

There is no doubt that diatoms are unique organisms with wonderful talents. Their success as primary producers is well known. An examination of the biomolecules which drive photosynthesis in diatoms however reveals some unexpected variety. Some proteins and pigments are very like those of green algae, others are reminiscent of red algae and others are simply unique. How did this “chimeric” collection come together in diatoms and why are they so successful? Obviously, one could conclude that all this was the product of choice and intelligent design. Others insist the diatoms have to be the product of evolution. Entering into the drama is endosymbiotic theory: it may seem improbable in the extreme, but it is the most popular choice available to evolutionists today.

The simplistic story of endosymbiosis is out. Evolutionists now accept multiple endosymbiotic events with most of the genes moving from the hostage into the host nucleus. Aside from questions as to how this migration could have happened and how the genes became safely incorporated into the host nucleus, there are serious questions concerning whether this is a realistic understanding of what we see today in plant cells.

Once molecular biologists had discovered that there is some DNA inside chloroplasts, this was assumed to be proof that endosymbiosis had occurred. 19 It soon became apparent, however, that most genes controlling the activities of the chloroplast, in fact, come from the host nucleus. This was the beginning of a realization of the scope of the problem where the majority of proteins needed by an organelle have to be transported into the organelle, and that is no mean task!

International trade

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)

Consider the case of Rubisco. This is the enzyme that catalyzes the first step in the photosynthetic conversion of carbon dioxide into sugar. Some have suggested that there is more Rubisco present in the world than any other enzyme. In green algae and land plants, Rubisco consists of eight large subunits encoded by a gene in the chloroplast and eight small subunits encoded by two adjacent genes in the nucleus.20

This means that not only are there some compounds essential to the functioning of the chloroplast which come from nuclear genes, but some of them are part of essential complexes that have to be assembled in the chloroplast once these components have managed to make it through the chloroplast membranes. It’s like a machine manufactured in one country that has to import its parts from another country, and pass all the security checks en route. Thus “most plastid proteins (over 90%) [in greens] are encoded by the nuclear genome and are imported into the plastid from the cytosol posttranslationally [after having been already synthesized].“ 21

Not only do essential proteins have to pass from the cytoplasm into the chloroplast in order for the chloroplast to function, but getting them into the chloroplast is also a complex process. As Lee et al. report, the “preproteins” (small subunit of Rubisco) that need to pass into the chloroplast are provided with a targeting signal tail of about 50-70 amino acid residues long. The preproteins are not yet folded; they are just a long string of amino acids whose targeting signal tail enable them to pass into the chloroplast. Once inside the chloroplast, other specialized enzymes have to cut off the transit peptide tail before Rubisco is assembled from the component parts.22

Beyond the Reach of Chance

These are processes today which require highly specific molecules to coordinate the details. Endosymbiotic events lack the capacity to provide these molecules from nothing, but they could not proceed without them. Every stage in a supposed endosymbiosis is much too specific to have proceeded through chance events. There is too much room for error. It does not make sense to use endosymbiotic theory to explain the unique features of diatoms. Rather, diatoms are a shining example of Intelligent Design.

Assortment of diatoms (Wikimedia Commons). The varieties in shapes and details are bewildering. Their geometric beauty surpasses any need for mere survival.



  1. Anne-Sophie Benoiston, Frederico M. Ibarbalz, Lucie Bittner, Lionel Guidi, Oliver Jahn, Stephanie Dutkiewicz and Chris Bowler. 2017. The evolution of diatoms and their biogeochemical functions. Trans. R. Soc. B 372: 20160397 pp. 1-10. http://dx.doi.org/10.1098/rstb.2016.0397
  2. Ryo Nagao et al. Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex. Nature Communications11: 2481 pp. 1-12. https://doi.org/10.1038/s41467-020-16324-3
  3. Autotrophs are photosynthesizers, they can supply their own nutrition.
  4. Nagao et al. 2.
  5. Nagao et al. 10.
  6. John M. Archibald. 2009. The Puzzle of Plastid Evolution. Current Biology 19: R81-R88. doi     1016/j.cub.2008.11.067
  7. Archibald p. R81.
  8. Archibald p. R83 and R84.
  9. Sergio A. Munoz-Gomez, Fabian G. Mejia-France, Keira Durnin, Morgan Colp, Cameron J. Grisdale, John M. Archibald, Claudio H. Slamovits. 2017. The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Current Biology 27: 1677-1684 http://dx.doi.org/10.1016/j.cub.2017.04.054
  10. Ahmed Moustafa, Bank Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya. 2009. Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms. Science 324 # 5935 1724-1726.  See p. 1724.  doi:10.1126/science.1172983
  11. Benoiston et al. 5-6.
  12. Benoiston et al. 6.
  13. Cheong Xin Chan, Adrian Reyes-Prieto, Debashish Bhattacharya. 2011. Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution. PLoS one 6 #12 e29138 11.  See p. 8. doi:10.1371/journal.pone.0029138
  14. Chan et al. 8, Benoiston et al. pp. 6 and 7.
  15. Philippe Deschamps and David Moreira. 2012. Reevaluating the Green Contribution to Diatom Genomes. Genome Biol. Evol. 4 #7: 683-688.
  16. Archibald p. R83.
  17. Archibald diagram p. R83.
  18. Benoiston et al. 6.
  19. Lynn Margulis. 1971. The Origin of Plant and Animal Cells. American Scientist 59: 230-235. See p. 231.
  20. Katie Wostrikoff and David Stern. 2009. In The Chlamydomonas Sourcebook: Organelles and Metabolic Processes. David Stern and David Stern (Editors). Vol. 2 Second edition. See p. 303.
  21. Dong Wook Lee, Sumin Lee, Young Jun Oh and Inhwan Hwang. 2009. Multiple Sequence Motifs in the Rubisco Small Subunit Transit Peptide Independently Contribute to Toc159-Dependent Import of Proteins into Chloroplasts. Plant Physiology 151: 129-141. See p. 129.  plantphysiol.org/cgi/doi/10.1104/pp.109.140673
  22. Lee et al. 129.

Margaret Helder completed her education with a Ph.D. in Botany from Western University in London, Ontario (Canada). She was hired as Assistant Professor in Biosciences at Brock University in St. Catharines, Ontario. Coming to Alberta in 1977, Dr Helder was an expert witness for the State of Arkansas, December 1981, during the creation/evolution ‘balanced treatment’ trial. She served as member of the editorial board of Occasional Papers of the Baraminology Study Group in 2001. She also lectured once or twice a year (upon invitation) in scheduled classes at University of Alberta (St. Joseph’s College) from 1998-2012. Her technical publications include articles in the Canadian Journal of Botany, chapter 19 in Recent Advances in Aquatic Mycology (E. B. Gareth Jones. Editor. 1976), and most recently she authored No Christian Silence on Science (2016) which promotes critical evaluation of scientific claims. She is married to John Helder and they have six adult children.

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