Chapter 17: Whole organism biotechnology

In this Chapter we examine the biotechnology that uses intact living organisms to produce commercially important products. In the main this means fungal fermentations in submerged liquid cultures, so we describe in detail the essential aspects of cultivating fungi: media, oxygen demand and supply, and fermenter engineering. We describe fungal growth pattern in liquid cultures; fermenter growth kinetics; growth yield; the stationary phase; and growth as pellets.

Beyond the batch culture, we discuss fed-batch methods, chemostats and turbidostats. Then we look towards the industrial scene and examine the uses of submerged fermentations, with the specific examples: alcoholic fermentations; citric acid biotechnology; penicillin and other pharmaceuticals; enzymes for fabric conditioning and processing, and food processing; steroids and use of fungi to make chemical transformations; the Quorn fermentation and evolution in fermenters; and the production of spores and other inocula. We hark back to ruminant digestion to consider the ‘engineering aspects’ of natural digestive fermentations in herbivores, and try to work out just how many anaerobic fungi we are cultivating in our livestock.

Many of the most important commercial (particularly food) fermentations take place in the solid state. So we look in a little more detail at the digestion of lignocellulosic residues, and then turn to our major foods: bread, cheese and salami manufacture; and soy sauce, tempeh and other food products. With a few comments about products like chocolate, coffee and even tea, which, though few people realise this, all depend on fermentation processes. Current opportunities and research challenges in fungal biotechnology (“the current fungal biotech revolution”) were discussed in the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019 (Meyer et al., 2020).

With the exception of the chytrids (the only true fungi with motile aquatic spores), filamentous fungi have evolved as terrestrial organisms designed to grow and degrade dead or sometimes living plant and animal biomass in terrestrial environments.

However, in biotechnology, fungi are generally grown in submerged culture, in tanks known as fermenters (Pirt, 1975; El-Mansi et al., 2007). This approach enables high levels of biomass and other products to be formed in a controlled environment. Note that in the United States the last two letters of this word distinguish the fermenter (the organism) from the fermentor (the cultivation apparatus) but we do not use that convention here.

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Updated December, 2020