Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s–1980s

Abstract

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as the “clean” Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered.

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Notes

  1. 1.

    “The secret world inside you,” exhibition at the AMNH, Nov. 7th, 2015–Aug. 16th, 2016; on Micropia, see the post on the microbiology blog “Small things considered” at http://schaechter.asmblog.org/schaechter/2016/01/take-your-kids-to-the-bugs-on-a-sunday-afternoon-micropia-the-worlds-only-microbe-zoo-in-amsterdam.html. Last access Aug 28th, 2017.

  2. 2.

    http://tumblr.amnh.org/post/142650634919/make-your-own-microbial-medley-a-famous.

  3. 3.

    “The microbiome of your gut”; “Make a home for microbes. How to make a Winogradsky column,” texts on the AMNH’s website at http://www.amnh.org/exhibitions/the-secret-world-inside-you/the-microbiome-of-your-gut; http://www.amnh.org/explore/ology/microbiology/make-a-home-for-microbes. Last access Mar. 29th, 2017). On microbial communities as models for ecosystems and life in general in recent science, Paxson and Helmreich (2014).

  4. 4.

    In an introductory essay to Bergey's Manual, the most important taxonomic reference work of microbiology, a microbial species has traditionally been defined as a distinct group of strains with distinguishing features and bearing close resemblance, which are “made up of the descendants of a single isolation in pure culture, and usually made up of a succession of cultures ultimately derived from an initial single colony” (Garrity et al. 2007, pp. 27–28).

  5. 5.

    On the “messy and polluted bacteriology” (Gradmann 2000), see next section. The term “pure culture era” was used by Cowan and Hill (1978); see Sect. 4.

  6. 6.

    On social and technological acceleration, see Rosa (2005) and my conclusion.

  7. 7.

    For brevity’s sake, scientists’ dates of birth and death are only provided where this is deemed relevant.

  8. 8.

    Some hints at the ambiguities inherent in this concept, which has always functioned as a stratagem to sort out bacteriologists, probably as much as bacteria, are provided by, for example, the concise summary on the topic in Lafar’s Handbuch der technischen Mykologie (1907), which sees Nägeli as much as Theodor Billroth, Edwin Klebs or Hallier as historical proponents of pleomorphism, but also concedes the confusion stemming from the fact that every researcher in the field would understand the concept differently from others. Lafar, standing firmly within the bacteriological framework of Pasteur and Koch (see below), suggests calling an organism pleomorphic if it possibly displays different self-contained cycles of development (“verschiedene in sich abgeschlossene Entwicklungskreise,” ibid., p. 47; unless indicated otherwise, all translations are mine). This comes closer to what “pleomorphism” may have referred to in discussions about bacterial variation in the 1920s and 1930s (Méthot 2015).

  9. 9.

    Serratia’s crimson-red growth on, for example, food had inspired tales of blood miracles over centuries, and therefore had great relevance to early nineteenth century protozoologists going back to Christian Gottfried Ehrenberg (1795–1876; Breed and Breed 1924).

  10. 10.

    Hansen’s approach represented a fusion of Pasteur, Brefeld, and Koch: Whereas it started with one selected cell (rather than obtaining isolation indirectly as Koch did for bacteria, by streaking them out), he also adapted Koch’s solid media. The concept of microbial purity as shaped in Europe also had an impact on Japanese fermentation technologies, where an interesting interplay of the purity ideal with traditional approaches using mixed microbial biota existed. See Ceccatti (2001), Lee (2015), and Teich (1983).

  11. 11.

    On pure lines in research on heredity, Müller-Wille (2007).

  12. 12.

    See, for example, Löffler (1983 [1887]), or William Bulloch’s History of Bacteriology (1938); Mazumdar (2002, pp. 98 f.) provides more references.

  13. 13.

    See, for example, Kostka (1924, p. 26); Hauduroy (1947, p. 200); Schröder (1975, p. 20, pp. 59–60); Madigan and Martinko (2006, pp. 119–120). For use of these methods in classification, see Sect. 3.

  14. 14.

    “Nicht zu verachten sind auch die moralischen Erfolge, die sich unwillkürlich bei der Beschäftigung mit der Reinkultur einstellen, wie der Sinn für peinliche Sauberkeit, die Stärkung der Ausdauer und der Geduld u. dgl. m.” (Richter 1907, p. 115).

  15. 15.

    Moreover, these tools have allowed classical bacteriology to spread around the world, when the equipment and instructions on proper usage, spread by, for example, Koch's famous courses, were transferred within Europe and to North America (Gossel 1989; Kreuder-Sonnen 2012).

  16. 16.

    On these fields, see Spath (1999) and O’Malley (2014).

  17. 17.

    “Was zunächst die Gewinnung des nöthigen Materials betrifft, so sind diese Bacterien, wie oben schon erwähnt, viel verbreiteter als man bisher glaubte. Einige von ihnen sind in jedem Sumpfe oder Teiche vorhanden, aber so spärlich, dass es nicht gelingt, dieselben bei directer mikroskopischer Untersuchung des Wassers und Schlammes aufzufinden. […] Dennoch habe ich das Vorhandensein von mehreren farblosen und rothen Arten im Teiche des Botanischen Gartens, […] constatiert, indem ich diese Organismen in Gefässen mit aus den betreffenden Orten entnommenem Wasser, Schlamm etc. spontan erscheinen liess. Ich verfuhr gewöhnlich auf die Weise, dass ich einige zerschnittene Stücke eines frisch herausgenommenen Butomus-Rhizoms mit dem an demselben anhaftenden Schlamm in ein tiefes, 3–5 Liter Wasser fassendes Gefäss legte und ein paar Gramm Gyps zusetzte. Nach 5-7 tägigem Stehen bei Zimmertemperatur beginnt die H2S-Entwickelung, wodurch zunächst der am Boden des Gefässes angesammelte Schlamm geschwärzt wird; dann fängt die Flüssigkeit allmählich an, von den unteren zu den oberen Schichten fortschreitend, infolge der Ausscheidung von Schwefel zu opalesciren, und endlich wird ein starker Geruch nach H2S bemerkbar; auf der Oberfläche bildet sich ein Häutchen welches aus Schwefel besteht. Nach 3-6 Wochen kann man schon bei mikroskopischer Untersuchung ohne Mühe einige Formen von Schwefelbacterien finden; weiterhin können sie sich unter Umständen ganz gewaltig vermehren.” (Winogradsky 1888, pp. 11–12).

  18. 18.

    Ackert (2012) and O’Malley (2014); see also the collection of enrichment methods from environmental microbiology and brewing compiled under the curious title Ökologie: Anhäufungen nach Beijerinck (“Ecology: Accumulations following Beijerinck”) by Stockhausen (1907).

  19. 19.

    “Sans entrer dans des details, ce n’est que le principe de la culture – dogme sacré de la religion microbiologique – qui m’intéresse à ce moment.” Undated annotated letter from Winogradsky to van Niel, presumably early 1932; “Imaginez un botaniste qui isolerait quelques plantes alpines de leur habitat naturel pour les cultiver dans une serre durant, disons, une trentaine d’années; en les comparant ensuite à leurs ancêtres sauvages et en ayant constaté que les caractères différentiels des espèces, si nets à l’origine, sont devenus brouillés, irait-il jusqu’à affirmer que ces caractères n’ont jamais existé? […] Et bien, je crois que le microbiologiste devrait aussi se garder d’une conclusion analogue en songeant que les 24 heures d’étuve comptent pour les microbes possiblement autant que toute une année pour une phanérogame.” Annotated letter from Winogradsky to van Niel, 9.7.1932; handwritten corrections of the typescript have been included. All letters from: Fonds Winogradsky WIN.2, Archives de l’ Institut Pasteur, Paris. Van Niel tried to establish pure cultures of environmental microbes at the time, using enrichment methods as a first step. He was interested in ecology and classification as well as in obtaining organisms to study certain physiological phenomena such as phototaxis or salt tolerance in the lab. On van Niel and the Delft school, see Spath (1999, Ch. 3.)

  20. 20.

    “Die langwierige Controverse über die Bacterienspecies muss damit als endgiltig abgeschlossen betrachtet werden.” Winogradsky (1888, p. 115).

  21. 21.

    Perkins (1928, p. 124). Richter (1907) makes a strong argument for the impact of pure culturing on the classification of various microbes, listing dozens of methods, many of which are variations of Koch's technique.

  22. 22.

    I will analyze the role of pure culture in classification for the American case, mostly for the reason of the availability of sources. Whereas different national and/or personal approaches to the subject existed in the first half of the century (see below), the situation became globally more homogenous after 1945, and the American institutions and manuals, such as Bergey's Manual of Determinative Bacteriology, were internationally authoritative.

  23. 23.

    Bergey (1923); further issues date from 1925, 1930, 1934, 1948, 1957, 1974, and 1984; for Bergey's history, see Murray and Holt (2001).

  24. 24.

    Committee on Bacteriological Technic (ed.) (1946). Similar to the descriptive charts and Bergey's, the Manual of Pure Culture Study developed into a successful, long-term publication. Reports read by Conn at the SAB's Annual Meetings on behalf of the Committee document the growth and revisions of the manual, as well as the numbers of copies being sold and the revenue generated for the society (e.g., Anon. 1931, p. 2). In 1946, the first bound volume was printed, to be followed by the re-named Manual of Microbiological Methods as a 7th edition in 1957 (Committee on Bacteriological Technic (ed.) 1957).

  25. 25.

    Conn, who also published a handbook on staining procedures, managed the publication of charts and manuals through a publisher at his home institution (Lillie 1977).

  26. 26.

    The era's onset depended on which species were considered. The term “pure culture era” seems to have been coined by Samuel T. Cowan (1905–1976), curator of the British National Culture and Type Collection (NCTC) and important bacterial taxonomist in the post-war decades. Cowan and Hill (1978, p. 12).

  27. 27.

    Fleck (2011, p. 108): “Jenes Züchten aus einem kranken Organismus ist nicht, wie das die klassische Bakteriologie will, eine Isolierung, die Gewinnung einer reinen Züchtung, sondern ein künstliches “Entbinden” aus dem Organismus, eine Umwandlung des Erregers in einen wilden Proteus.” The term Entbinden is German in the Polish original; the text was translated into German and republished in Fleck (2011).

  28. 28.

    For further detail on environmental microbiology and microbial ecology, see Ackert 2013; O’Malley 2014.

  29. 29.

    The symposium’s title was “Anreicherungskultur und Mutantenauslese” (enrichment culture and mutant selection); see Schlegel (1965).

  30. 30.

    The concept is used in taxonomy also by, for example, Starr et al. (1981, p. 155).

  31. 31.

    Staley and Konopka (1985) trace this observation back to Winogradsky’s students in the 1930s.

  32. 32.

    Such as, for example, the proposal of the Archaea as a third domain of life on the basis of RNA analyses around 1980 (Sapp 2009) or the blurring of species boundaries such as between the enteric bacteria Escherichia and Shigella (Lan and Reeves 2002).

  33. 33.

    “Whenever possible, the type of a species or subspecies is a designated strain. A type strain is made up of living cultures of an organism which are descended from a strain designated as the nomenclatural type. The strain should have been maintained in pure culture and should agree closely in its characters with those in the original description (see Chapter 4C). The type strain may be designated in various ways (see Rule 18b, c, and d). For a species which has not so far been maintained in laboratory culture or for which a type strain does not exist, a description, preserved specimen, or illustration (see also Rule 18f) may serve as the type” (Lapage et al. 1992, Rule 18a).

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Acknowledgement

I would like to thank the editors of this special issue, Robert Meunier and Kärin Nickelsen, as well as two reviewers for their comments and suggestions. I am also grateful to The American Society of Microbiology Archives, and especially Jeff Karr, for help and access to materials, and the permission to reproduce a figure from society publications. Warwick Anderson provided an inspiring comment at a moment when my only task was to shorten the manuscript, and which thus has to be spelled out elsewhere.

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Grote, M. Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s–1980s. HPLS 40, 11 (2018). https://doi.org/10.1007/s40656-017-0175-9

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Keywords

  • Microbiology
  • Pure culture
  • Purity
  • Classification
  • Microbial ecology
  • Petri dish
  • Winogradsky column