Decade in Review
Since our last post we welcomed in a new year and a new decade, so we want to take the opportunity to reflect on some of the great diatom science from the 2010s. This month Nick Schulte, with input from the rest of the DOM editorial board, put into the spotlight a paper or project per year to give an idea of some of the impressive, diverse science our community – from early-career researchers to senior diatomists – developed in the last decade.
2010: Diatoms of the United States (a.k.a. Diatoms of North America)
Spaulding, S. A., Lubinski, D. J., & Potapova, M. (2010). Diatoms of the United States.
The start of the decade brought us a project that is still, in 2020, changing the way we identify diatoms and understand diatom taxonomy and ecology. Diatoms of the United States (now Diatoms of North America) really began from the course materials produced by instructors of the Ecology and Systematics of Diatoms course at Iowa Lakeside Laboratory. The initial DOTUS website launched on 01 June 2010 via www.westerndiatoms.colorado.edu as a “diatom identification guide & ecological resource for water resource managers, ecologists, taxonomists, analysts, systematists, students, and the public.” At release, DOTUS included a whopping 25 species pages! Ten years later, it has catalogued 975 species with more being added regularly by over 140 taxon contributors, many of whom are Lakeside Lab alumni. And that’s not even mentioning the wealth of general diatom information, ecological data, and other resources provided by the website and its editorial board.
The Diatoms of North America project is truly a unique resource for scientists and managers, and it serves as a model for diatom identification and ecological resources globally in the 2020s and beyond.
You can read here our DOM post from November 2018 spotlighting Diatoms of North America.
Figure 1. The original homepage of Diatoms of the United States in 2010. For a blast from the past, check out DOTUS on the Way Back Machine.
Some of our other favorites
Theriot, E. C., Ashworth, M., Ruck, E., Nakov, T., & Jansen, R. K. (2010). A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research. Plant Ecology and Evolution, 143(3), 278-296.
2011: Diatoms and animals linked by…urea?
Allen, A. E., Dupont, C. L., Oborník, M., Horák, A., Nunes-Nesi, A., McCrow, J. P., … & Bowler, C. (2011). Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature,473(7346), 203-207.
In 2011, Andy Allen and colleagues found that diatoms have a urea cycle, a process that was, prior to this work, thought to have originated in metazoans. Allen’s team used the marine diatom Phaeodactylum tricornutumand a variety of cutting-edge techniques (genomics, metabolomics) to show the ornithine-urea cycle was evolved in the secondary endosymbiotic host (exosymbiont) before plastid acquisition, hence why it is absent in green algae and plants.
Their results determined the urea cycle is integrated into core carbon and nitrogen metabolic processes. The ornithine-urea cycle is particularly important in the redistribution and turnover of inorganic carbon and nitrogen into cellular components (e.g., proline and glutamine) that are critical metabolites for cell wall formation. This study implicates the urea cycle as a critical feature of the proliferation of diatoms after upwelling events and, likely, the dominance of diatoms in the modern ocean.
Some of our other favorites
Hamsher, S. E., Evans, K. M., Mann, D. G., Poulíčková, A., & Saunders, G. W. (2011). Barcoding diatoms: exploring alternatives to COI-5P. Protist, 162(3), 405-422.
Kamp, A., de Beer, D., Nitsch, J. L., Lavik, G., & Stief, P. (2011). Diatoms respire nitrate to survive dark and anoxic conditions. Proceedings of the National Academy of Sciences, 108(14), 5649-5654.
Trobajo, R., Rovira, L., Mann, D. G., & Cox, E. J. (2011). Effects of salinity on growth and on valve morphology of five estuarine diatoms. Phycological Research, 59(2), 83–90.
2012: Diatoms + bacteria = <3
Amin, S. A., Parker, M. S., & Armbrust, E. V. (2012). Interactions between diatoms and bacteria. Microbiol. Mol. Biol. Rev., 76(3), 667-684.
Although we haven’t focused much on marine diatoms in this blog (yet), this paper by Amin and colleagues summarizes information that is useful beyond oceanic systems. This work is an invaluable synthesis of diatom-bacteria interactions, identifying core features of their observed and potential exchanges. Here, they focused on interactions at the single diatom cell level. Among the takeaways are that a small subset of heterotrophic bacteria are strongly associated with marine diatoms, with coevolved communication mechanisms with members of such genera as Roseobacter, Sulfitobacter, and Flavobacterium. These bacteria share with diatoms vitamins, iron and other trace elements, and dissolved carbon and nitrogen. This detailed review set the stage for continued work on how these interactions and resultant processes that were developed over evolutionary time scales will be affected by contemporary climate change and human disturbance.
Figure 2. A real conversation between a diatom and a bacterium. No cameras were allowed in the sea, so sketch artist and co-editor Nick Schulte may have taken some liberties so as to get more clicks.
Some of our other favorites
Hildebrand, M., Davis, A. K., Smith, S. R., Traller, J. C., & Abbriano, R. (2012). The place of diatoms in the biofuels industry. Biofuels, 3(2), 221-240.
Rimet, F. (2012). Recent views on river pollution and diatoms. Hydrobiologia, 683(1), 1-24.
Wetzel, C. E., de Bicudo, D. C., Ector, L., Lobo, E. A., Soininen, J., Landeiro, V. L., & Bini, L. M. (2012). Distance Decay of Similarity in Neotropical Diatom Communities. PLoS ONE, 7(9).
2013: An inordinate fondness for beetlesdiatoms
Mann, D. G., & Vanormelingen, P. (2013). An inordinate fondness? The number, distributions, and origins of diatom species. Journal of Eukaryotic Microbiology, 60(4), 414-420.
How many diatoms are there? As diatom researchers, each of us probably throws out numbers anywhere between 12,000 and half a million.
David Mann and Pieter Vanormelingen open their 2013 article with the apocryphal quote of J. B. S. Haldane that the Creator must have an inordinate fondness for beetles, setting up the argument that diatoms are the beetles of the algal world. That is, by their calculations, there are likely up to 100,000 extant diatom species (still not quite up to The Beetles’ ~350,000). They arrive at that estimate by (1) considering the rate of species description, (2) new morphospecies or molecularly-identified species (e.g., environmental DNA), (3) phenotypic plasticity, and (4) geographic and habitat sampling bias. They go on to discuss the context of this enumeration in terms of biogeography (patriots or tramps) and evolution. All in 5 pages!
In this paper, Mann and Vanormelingen do an admirable job of dissecting the characteristics of a total species number estimate, particularly being the first to intensively consider the ramifications of molecular identification of new taxa. And they also synthesize available work on dispersal and speciation to give us a conceptual framework for diatoms as intermediate dispersers with populations undergoing speciation.
Some of our other favorites
Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Humbert, J. F., & Bouchez, A. (2013). Next‐generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular Ecology Resources, 13(4), 607-619.
2014: Is that snot on the rock? Didymo’s story
Bothwell, M. L., Taylor, B. W., & Kilroy, C. (2014). The Didymo story: the role of low dissolved phosphorus in the formation of Didymosphenia geminata blooms. Diatom Research, 29(3), 229-236.
We wanted to highlight the world’s potentially most (in)famous diatom, Didymosphenia geminata, in our Decade-In-Review. This review by Max Bothwell and colleagues does a great job of summarizing the extensive work on “rock snot” in the 21st century. Didymo’s wide geographic spread is complicated, but this paper distills some of that complexity down to two major factors: human-mediated introduction and very low soluble reactive phosphorus as a proximate cause of bloom formation. Bothwell et al. discuss/hypothesize how increased prevalence of Didymo blooms can likely be attributed to oligotrophication caused by any of four human disturbances at the global scale. If you’re not familiar with the Didymo story, or want to investigate some of the unknowns about this blooming taxon yourself, this is a great place to start.
Figure 3. “Once upon a time there was a diatom known as Didymospenia geminata, but all its friends called it Rock Snot. Rock Snot didn’t like its nickname – it preferred Didymo. Didn’t they all realize how embarrassing it was to secrete tons and tons of extracellular polymeric substances all over the rocks when the phosphorus got too low? You didn’t see Didymo go around calling its friend Gomphonema parvulum “Identity Crisis,” did you? Or Microcystis aeruginosa “Dog Killer,” eh? No, Didymo was much too nice for that, however apt those nicknames would be. And, besides, was it really Didymo’s fault that the phosphorus was too low in the water? Maybe the humans should have thought twice before they put all that nitrogen on the land in the first place. But, no, let’s blame your friendly diatom and call it names. And, come to think of it, did anyone even think of asking Didymo if it wanted to take a trip to New Zealand? Maybe it was perfectly fine staying put, staying home. But, like many great adventures, I guess Didymo’s unexpected travel is where this story starts…” [Excerpt from the upcoming bestseller (if it’s ever written) Once Upon A Time: The Tale of Didymo, A Not-So-Snotty Diatom]
Some of our other favorites
Abarca, N., Jahn, R., Zimmermann, J., & Enke, N. (2014). Does the cosmopolitan diatom Gomphonema parvulum(Kützing) Kützing have a biogeography?. PLoS One, 9(1).
Lazarus, D., Barron, J., Renaudie, J., Diver, P., & Türke, A. (2014). Cenozoic planktonic marine diatom diversity and correlation to climate change. PLoS One, 9(1).
2015: Scanning diatoms like you’re at the grocery store
Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B. (2015). Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Molecular Ecology Resources, 15(3), 526-542.
Metabarcoding is a method of using small regions of DNA to identify organisms in an environmental sample. This technique saw an uptick in use in the 2010s. Zimmermann and colleagues were among the first to address the million dollar question: how does metabarcoding compare to morphological identifications in assessing diatom diversity? Looking at a mock community with known morphospecies, they determined a rbcL amplicon was the most effective at recovering species-level diversity. DNA-based diatom assessments are a continually evolving area, with a current emphasis on understanding how it compares to traditional diatom methods. This work by Zimmermann et al. is one of the key building blocks in a future of metabarcoding in diatom-based environmental work that maintains a connection to past (and current) techniques.
Figure 4. What metabarcoding could look like in today’s commercialized society. Get your Luti-Cola while it’s on sale!
Some of our other favorites
Rühland, K. M., Paterson, A. M., & Smol, J. P. (2015). Lake diatom responses to warming: reviewing the evidence. Journal of Paleolimnology, 54(1), 1-35.
2016: Tracking climate change from lake sediments
Boeff, K. A., Strock, K. E., & Saros, J. E. (2016). Evaluating planktonic diatom response to climate change across three lakes with differing morphometry. Journal of Paleolimnology, 56(1), 33-47.
In the 2010s the relationships between diatoms and climate change were a hot topic, at both contemporary and historical time scales. Kelsey Boeff and colleagues looked at sediment cores from three northeast USA lakes to evaluate the effects of lake morphometry and local processes on diatom response to climate change. Across the study region there were declines in wind speed and ice-out date in the 1900s, and each lake varied morphometrically. Boeff et al. constructed a diatom-inferred stratification index that included indicator taxa Aulacoseira subarctica and Discostella stelligera to reconstruct lake thermal stratification patterns. They found that the lakes differed in thermal structure and diatom response to climate forcings, which was attributed to differences in lake morphometry and sedimentation rates and the timing of D. stelligera blooms. This work demonstrated the importance of combining past and present diatom observations to more fully understand community responses to climate change.
Some of our other favorites
Malviya, S., Scalco, E., Audic, S., Vincent, F., Veluchamy, A., Poulain, J., … & Zingone, A. (2016). Insights into global diatom distribution and diversity in the world’s ocean. Proceedings of the National Academy of Sciences, 113(11), E1516-E1525.
Medlin, L. K. (2016). Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence. Phycologia,55(1), 79-103.
Ruck, E.C., Nakov, T., Alverson, A.J. and Theriot, E.C. (2016) Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales. Molecular Phylogenetics and Evolution 103: 155–171. DOI: 10.1016/j.ympev.2016.07.023
Soininen, J., Jamoneau, A., Rosebery, J., & Passy, S. I. (2016). Global patterns and drivers of species and trait composition in diatoms. Global Ecology and Biogeography, 25(8), 940-950.
2017: Look within the species
Godhe, A., & Rynearson, T. (2017). The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments. Philosophical Transactions of the Royal Society B: Biological Sciences, 372(1728), 20160399.
Much of diatom-related ecological work considers diatom communities (co-occurrent populations of multiple species). In this review, Godhe and Rynearson demonstrate the importance of considering population- and metapopulation-level variation in explaining ecological patterns and processes. Godhe and Rynearson show that intraspecific variation within diatoms is prolific, structured, and is likely a driving force in individual species survival in and adaptation to variable environments. They emphasize that there is variation in natural populations in genes related to carbon metabolism that are likely to affect species success in environments with elevated CO2. Altogether, this work emphasizes the need to consider intraspecific variation in ecological diversity and response to human disturbances.
Some of our other favorites
Apothéloz‐Perret‐Gentil, L., Cordonier, A., Straub, F., Iseli, J., Esling, P., & Pawlowski, J. (2017). Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring. Molecular Ecology Resources, 17(6), 1231-1242.
Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., … & Allen, A. E. (2017). Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature, 541(7638), 536-540.
2018: Diatoms pumping that carbon
Tréguer, P., Bowler, C., Moriceau, B., Dutkiewicz, S., Gehlen, M., Aumont, O., … & Jahn, O. (2018). Influence of diatom diversity on the ocean biological carbon pump. Nature Geoscience, 11(1), 27.
Another heavy-hitting marine diatom review paper in the spotlight surely means we’ll need to have some future posts on marine taxa/processes. This one by Tréguer and colleagues addresses how diatom diversity affects the ~40% of primary productivity and particulate carbon export to ocean depths. They showed that contribution to the carbon pump varies by morphology (size, shape), the Si/C ratio of diatom cells, the thickness of the frustules, life history stage, biotic interactions, and lineage. Furthermore, they discuss the ramifications of climate change on diatom primary production, with model simulations projecting a decline in all areas other than the Southern Ocean. Alongside conceptual models, this paper provides detailed methodological and synthetic information on the contribution of diatoms to global carbon cycling that can be applied across ecosystems.
Figure 5. Artist rendering of the ocean biological carbon pump and the role of diatoms
Some of our other favorites
Jamoneau, A., Passy, S. I., Soininen, J., Leboucher, T., & Tison‐Rosebery, J. (2018). Beta diversity of diatom species and ecological guilds: Response to environmental and spatial mechanisms along the stream watercourse. Freshwater Biology, 63(1), 62-73.
Spanbauer, T. L., Fritz, S. C., & Baker, P. A. (2018). Punctuated changes in the morphology of an endemic diatom from Lake Titicaca. Paleobiology,44, 89–100.
2019: Freshwater vs. marine diatoms
Nakov, T., Beaulieu, J. M., & Alverson, A. J. (2019). Diatoms diversify and turn over faster in freshwater than marine environments. Evolution, 73(12), 2497-2511.
In this paper, Nakov and colleagues do not necessarily pit freshwater diatoms against marine diatoms (a battle for control of planet Earth!), but rather look at diatom evolution along the marine-freshwater and plankton-benthos divides. To do this, they estimated rates of colonization and diversification using a time-calibrated phylogeny representing extant diatom diversity. This endeavor was largely driven by the observation that there are many more freshwater species than marine, with the question of, “Why?”. In short, the imbalance between freshwater and marine species richness is because of faster turnover and faster net diversification in freshwaters for both planktonic and benthic habitats. Particularly important in arriving at this conclusion was the consideration of many potentially interacting traits and environmental factors beyond those traditionally seen as important. This paper not only applies new techniques and perspectives to old questions, it draws attention to the evolutionary connectivity of freshwater and marine diatoms that we should all bear in mind as a global diatom research community.
Some of our other favorites
Szabó, B., Lengyel, E., Padisák, J., & Stenger-Kovács, C. (2019). Benthic diatom metacommunity across small freshwater lakes: driving mechanisms, β-diversity and ecological uniqueness. Hydrobiologia, 828(1), 183-198.
Valentin, V., Frédéric, R., Isabelle, D., Olivier, M., Yorick, R. and Agnès, B., (2019). Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France Water Framework Directive networks. Metabarcoding and Metagenomics, 3, p.e39646.
Soininen J, Teittinen A. (2019). Fifteen important questions in the spatial ecology of diatoms. Freshwater Biology, 64, 2071–2083.
In summary
Looking at only one paper a year clearly doesn’t capture all of the great research and syntheses produced this past decade, but hopefully this whets your appetite to do your own reflection on diatom science in the 2010s. If we missed any of your favorites, let us know in the comments below, on Facebook, or via Twitter.
We also realize we committed to trying to release these blog posts more regularly on the last Monday of each month, as well as try to do a month-in-review of new articles. Neither of those happened this month – New Year’s resolutions are hard to keep, even for diatomists. But we’re hoping to be better in the ensuing posts. By the way, do get in touch to offer your creative genius to write one of this year’s posts. Happy 2020 and new decade, everyone!