1.7 Microbial diversity in general

Micro-organisms exist in every conceivable place on Earth, even in extreme environments. The tropics are considered to be richer in microbial species diversity than the temperate zones, but deserts may feature an equal amount, if not more, microbial diversity, and microbial communities can be found on rocks and within deep rock crevices (e.g. Staley et al., 1982). Temperature may be the only limitation as to where they can and cannot exist and/or function (Hunter-Cevera, 1998).

Micro-organisms exist in every conceivable place on Earth, even in extreme environments. The tropics are considered to be richer in microbial species diversity than the temperate zones, but deserts may feature an equal amount, if not more, microbial diversity, and microbial communities can be found on rocks and within deep rock crevices (e.g. Staley et al., 1982). Temperature may be the only limitation as to where they can and cannot exist and/or function (Hunter-Cevera, 1998).

The conservative estimate is that there are 1.5 million species of fungi on Earth, of which only 120,000 species have been isolated or described (Hawksworth, 1997, 2001; Hawksworth & Lücking, 2017). The former estimate was made by comparing the number of species of fungi and vascular plants described for particular geographic regions. For example, in the British Isles there are about six times more species of fungi than species of vascular plants. Extrapolating this ratio to the 270,000 species of vascular plants in the world gives an estimate of 1,620,000 fungi. Now, this figure needs to be corrected (to 1,504,800) to account for the double counting of fungal species resulting from the practice of giving separate specific names to the asexual and sexual stages of some fungi (because it may not be known that the two reproductive stages belong to the same fungus). In recent years molecular approaches to species recognition, together with the recognition of new habitats, hyper-diverse environments and unstudied collections have prompted revision of this conservative estimate of fungal diversity. Hawksworth & Lücking (2017) conclude that the range 2.2 to 3.8 million species of fungi on Earth is a better estimate. They point out that this means that ‘…at best just 8%, and in the worst case scenario just 3%...’ of the world’s fungi have been formally described and named so far. You might well ask: ‘Where are the other 92 to 97% of undescribed fungi?’

In fact, recent developments of molecular phylogeny have revealed an unexpected diversity, many times greater than this, among fungi, and indeed, most other organisms. We mentioned in the previous Section the numerical discrepancy between living presence detected by environmental DNA testing and culturability (as illustrated in Fig. 1 in the previous section). Applying molecular phylogenetics to the DNA testing identifies many cryptic species (species recognised only by analysis of DNA sequences). Based on such data, the number of fungal species on the Earth has been estimated to be 12 (11.7-13.2) million compared to the estimate of 2.2-3.8 million species indicated above (Wu et al., 2019). Intensive studies of specific fungal genera and families have demonstrated that in countries and areas that were hitherto neglected by mycological taxonomists, up to over 90% of the collected specimens may constitute undescribed species (Hyde et al., 2018). But the novelty goes beyond recognising more species; a number of novel taxa including new divisions, classes, orders and new families have been established in the last decade by molecular phylogenetics, and many of these dark matter fungi belong to early diverging branches of the fungal tree (Grossart et al., 2016). The range and prevalence of the genetic material being detected has led to it being called biological dark matter [https://en.wikipedia.org/wiki/Biological_dark_matter] by (informal) analogy with cosmological dark matter, which is a form of invisible matter thought to account for approximately 85% of the matter in the universe because of its gravitational influences. Biological dark matter is an extremely active and important research topic, which we cannot pursue further here but we do suggest a few representative references: Wu et al., 2011; Carey, 2015; Lok, 2015; Wu et al., 2019.

Part of the answer to our question about the location of all those undescribed fungi is that there are not many mycologists in the world today and not much work has been done in several unique geographical regions or habitats. Many ‘missing fungi’ may be associated with tropical forests, for example. Insects may be another large source of missing fungi as many fungi are already known to be associated with insects. Finally, many missing fungi may be discovered in specialised habitats which have not yet been explored at all, or have been only poorly investigated. The rumen and hindguts of herbivorous animals and the inner surfaces of Antarctic rocks do not sound like very promising habitats, but they are examples of habitats that have, unexpectedly, already yielded novel fungi.

Wherever they occur, fungal communities are very diverse metabolically, physiologically and taxonomically (Bass & Richards, 2011; Money, 2014). Given the benefits that man has derived from the fungi we know about, it is surprising, and disappointing, that more efforts have not been made to seek out these still unisolated fungi.

Resources Box

About the diversity of fungi

We do not intend to expand further on the topic of fungal biodiversity here because we prefer to concentrate on other particular aspects of the fungal contribution to the soil community, but if you wish to investigate fungal diversity now CLICK HERE to see our page of recommended literature references.

Updated October, 2019