Biodiversity and Conservation Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate? --Manuscript Draft-Manuscript Number:
BIOC-D-12-05134R1
Full Title:
Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate?
Article Type:
SI: Tropical Fungi
Keywords:
Biodiversity * Conservation * Cryptic species * Environmental sequences * Fungal:plant ratios * Inventorying * Undiscovered species
Corresponding Author:
David Hawksworth Universidad Complutense de Madrid, Facultad de Farmacia Madrid, SPAIN
Corresponding Author Secondary Information: Corresponding Author's Institution:
Universidad Complutense de Madrid, Facultad de Farmacia
Corresponding Author's Secondary Institution: First Author:
David Hawksworth
First Author Secondary Information: Order of Authors:
David Hawksworth
Order of Authors Secondary Information: Abstract:
Recent estimates of the global species numbers of fungi suggest that the much-used figure of 1.5 million is low, and figures up to 5.1 million have been proposed in the last few years. Data emerging from tropical studies and from large-scale sequencing of environmental samples have the potential to contribute to progress towards a more robust figure. Additional evidence of species richness is coming from long-term studies of particular non-tropical sites, and also from molecular phylogenetic studies revealing extensive cryptic speciation. However, uncertainties remain over fungus:plant species ratios and how they should be extrapolated to the global scale, and also as to the geographical distribution of fungi only known as sequences. Also unclear is the extent to which figures should be modified to allow for insect-associated fungi. The need for comprehensive studies, especially in the tropics, to address the uncertainties used in past extrapolations is stressed. For the present, it is recommended that the phrase "at least 1.5, but probably as many as 3 million" be adopted for general use until some of the current uncertainties are resolved.
Response to Reviewers:
Thanks for this. The comments were much appreciated and certainly led to me making some further clarifications and explanations. Editors comments: P1L18 - Change '5.1' to '5.1 million' DONE P1L24 - Please can you be more precise in your use of the wording 'additional evidence of species richness' DONE P4L19 - Change 'data on' to 'data relating to' DONE P4L21 - Change 'global species' to 'global fungal species' DONE P4L25 - Change 'species' to 'fungal species' DONE P4L35 - Change 'those that' to 'those species that' DONE P5L2 - Change to 'M. C. Aime' DONE P5L53 - Change 'rations' to 'ratios' DONE P6L58 - Buee et al (2009) New Phyt 184, 452-459 is a more appropriate reference than Lentendu et al 2011 DONE – but I kept the Lentendu one as well as it includes a useful summary of studies made. P7L9 - You could replace 'new' with 'next' or 'new/next' DONE
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P8L46 - Change 'that' to 'which' CHANGED, but the other way round! P11L39 - lover case first letters for 'earth' and 'ocean' I was following the authors' usage but have changed P12L8 - accidental upper case C in 'Schoch' DONE Reviewer #1: This was an enjoyable summary and disucssion of the most recent literatrue on the topic of estimating fungal divesity and should be pulished with very minor changes. Two thougths came to mind as I was reading this review: 1) While there are contiuous discoveries of large numbers of fungi in soil via moleuclar studies, there are not similar discoveries in marine sediments. I do not know if this is due to investigators looking in marine sediments and not finding any fungi or if there is an assumption that there are few fungi in marine sediments so no one bothers to look. If the author knows what the situation is it would be great to add a sentence or two about this topic. I added a couple of sentences and three references – I checked Gareth's paper in the issue and found he did not refer to those so it may be useful to have done that! 2) One fundamental issue with the fungus:plant speices richenss ratios is that of geogaphic distribution. If fungi and plants have similar sized ranges you would expect that as the % turnover in plant species from one area to the next would be mirrored in a similar % turnover in fungi,and the fungus:plant ratios would be similar accross various scales. On the other hand if the average ranges are quite different, than the ratios would not scale up well at all. The author discusses the need for more studies in the tropics and accross spatial scales, but I think that adding a sentence or two on the issues of extrapolating from local studies to region or global estimaes would be benifical. I added some more comments about this in the final section. minor editorial changes page 2, line 56-58: "species numbers that had not previously used by mycologist" either "species numbers not previously.." or "previously been used". DONE page 4, line 29 should be "... subject to repeated visits, even over 40 years, has the ... DONE
Reviewer #2: This paper provides a thoughtful summary of recent estimates of fungal species richness, and outlines particular topics (the sampling of different geographic regions, cryptic species, fungal:plant ratios etc) that may influence our estimates of fungal diversity. The paper is well-written, and should prove interesting to fungal biologists as well as those working in wider areas of ecology and conservation. However, to place the paper more in context, a few sentences in the introduction explaining why it is important to reach a robust estimate of fungal richness, particularly for conservation purposes, may be beneficial. Only one minor point: there is an extra 'a' on page 7, line 18, which needs to be removed: "...do not correspond to any allocated 'a' scientific name in GenBank..." I could not see the reason for this; seems accurate as it is.
Reviewer #3: General comments This paper is a reassessment of global estimates for fungal diversity and a call for continuity in the scientific community in proclaiming global diversity estimates of fungi. Overall, this is a useful paper that provides updated statistics on fungal richness estimates and highlights ecosystems that have been intensively surveyed. While I understand the significance of having a golden number that is an estimate of all fungal diversity, it is not clear to me why fungal:plant ratios are the best method of estaimation. A discussion of the utility and limitations of using fungal:plant ratios would be valuable, as I imagine that using fungal:plant ratios would be appropriate for some Powered by Editorial Manager® and Preprint Manager® from Aries Systems Corporation
fungal groups, but not for others. I think it would also be useful to have a breakdown of fungal diversity estimates for the various fungal groups. For example, it would be great to see a table with an estimate of total AM fungi, total ECM fungi, total decomposer fungi, total endophytic fungi, pathogens, etc. with references and methods of estimation. It would be interesting to see if the plant:fungal ratios calculated for specific fungal groups are consistent across biomes. Within-group variation may be where some of the inconsistency in global diversity estimates is derived from. This would be nice to do but is beyond the scope of this summary as it would take much work to find any meaningful data on most of these categories. Pg 2 Ln 35-42: This sentence needs to tie the Blackwell study back to the big picture of the paper, as it begins a new section. The first sentence does not tell the reader what Blackwell's citations relate to. DONE Pg 2 Ln 56-58: Again, the first sentence of this paragraph does not clearly lay out what the Mora paper set out to do. What does, "included fungi in an approach" mean? Was it a study of many different organisms or was it just another attempt to estimate fungal diversity? Readers should not have to refer back to original articles or have to read on in the paragraph to get this type of information. DONE Pg 6 Ln 48-49: A better explanation is needed for the 5X correction factor. DONE Pg 7 Ln 43-47: A brief overview of the various sides of the debate would be useful for readers (in a couple of short sentences). DONE Pg 7 Ln 52-56: The current estimation should be included in the beginning of this paragraph so that readers can quickly find information on the updated figures. DONE Pg 8 Ln 49-55: I strongly suggest that an emphasis be placed on how inventory surveys are not a priority for most funding agencies, and that resources should be allocated for this purpose. DONE
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Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate? David L. Hawksworth
Abstract Recent estimates of the global species numbers of fungi suggest that the much-used figure of 1.5 million is low, and figures up to 5.1 million have been proposed in the last few years. Data emerging from tropical studies and from large-scale sequencing of environmental samples have the potential to contribute to progress towards a more robust figure. Additional evidence of species richness is coming from long-term studies of particular nontropical sites, and also from molecular phylogenetic studies revealing extensive cryptic speciation. However, uncertainties remain over fungus:plant species ratios and how they should be extrapolated to the global scale, and also as to the geographical distribution of fungi only known as sequences. Also unclear is the extent to which figures should be modified to allow for insect-associated fungi. The need for comprehensive studies, especially in the tropics, to address the uncertainties used in past extrapolations is stressed. For the present, it is recommended that the phrase "at least 1.5, but probably as many as 3 million" be adopted for general use until some of the current uncertainties are resolved.
Keywords Biodiversity · Conservation · Cryptic species · Environmental sequences · Fungal:plant ratios · Inventorying · Undiscovered species
D. L. Hawksworth Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, 28040, Madrid. Spain Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK e-mail:
[email protected]
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Introduction The conservative global estimate of 1.5 million species of fungi, published just over 20 years ago (Hawksworth 1991), has come to be regularly cited in both scientific and semi-popular literature. That figure was considered to be, if anything, an underestimate at the time, and also utilized extrapolations based on low estimates for the global numbers of vascular plant species. When I revisited the topic ten years later (Hawksworth 2001), I pointed out that with the additional records of UK fungi that had accrued, and the upward revision of estimated global vascular plant species numbers, it could be argued that the 1.5 million figure should be raised to 2.3 million. Nevertheless, in view of uncertainties over the justification for extrapolations, especially in view of the limited information available from the tropics, it appeared prudent to continue to commend 1.5 million as a working hypothesis. The object of this paper is to consider recent contributions to the debate and, in particular, the extent to which additional data from the tropics and molecular studies may be assisting progression towards a more robust estimate for the global number of fungal species.
Recent estimates Blackwell (2011) prepared a detailed and valuable overview of estimates of global species numbers of fungi, citing many pertinent publications, especially ones which appeared during the last ten years. Consequently, it would be superfluous to revisit all of those here, and her study should be read in conjunction with the present one for those seeking such an overview. Blackwell noted that estimates up to 5.1 million had been published. The higher figure came from the study of O'Brien et al. (2005) who made global extrapolations from large-scale sequencing of the fungi in two plots from different parts of a forest in North Carolina (USA); that study is commented on further below. However, Blackwell did not commend a particular number as a working estimate, but rather stressed the need for many more biologists to work on fungi and for methods to be found to handle the overwhelming diversity being discovered through sequencing environmental samples. Mora et al. (2011) included fungi in an approach to determining species numbers of all eukaryotic organisms on Earth that had not previously been used by mycologists. They
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found that there were predictable patterns in the recognition of taxa in the rank of genus 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
and above in well-studied groups of organisms; those patterns were applied to the fungi and other less-studied groups to provide estimated species numbers. In the case of the fungi, using a figure of 43,271 for the species catalogued, they predicted that the total number of fungal species should be 611,000 (S.E. ± 297,000), suggesting that around 7 % (range 5.5–13 %) were known. The fungal data set, including the number of species, that these authors used was unfortunately taken only from the Catalogue of Life metadatabase (www.catalogueoflife.org), while a figure of around 100,000 for the number of described fungal species is generally accepted (Kirk et al. 2008). While the percentage results may have some informative value, that could change had a more complete fungal dataset been used. This is especially so as new higher level fungal taxa, at ranks such as phylum and class, continue to be recognized. It would, therefore, be unwise to accord too much significance to the estimate presented in Mora et al. (2011). This conclusion was also reached by Bass and Richards (2011), who considered that the paper should be viewed as a "call-to-arms" for a concerted and continued effort to improve our knowledge of fungal diversity, thus echoing the sentiments of Blackwell (2011). Bass and Richards (2011) also reviewed the current state of knowledge, drawing attention to their own contribution to the discovery and recognition of the new phylum Cryptomycota (Jones et al. 2011), and the recent recognition of new fungal classes (Archaeorhizomycetes, Rosling et al. 2011, as well as an unnamed Soil Clone Group II). They noted that the two main bases for estimating fungal diversity were: (1) the number of described species and their taxonomic structure; and (2) extrapolating species number:area relationships, from regional to global scales. Their conclusion, with which most mycologists would concur, was that knowledge of fungal taxonomy and environmental sampling was currently too incomplete for either approach to be reliable. With respect to possible global species numbers they nevertheless concluded that it was likely that the true number of species on Earth was a seven-digit number, although it could even be an order of magnitude higher. There are at least two pertinent papers not cited in the above three studies. First, Adl et al. (2007) provide a table which summarises estimated species numbers in protistan groups, which gives the potential number of fungal species as "n x 106", i.e. an unspecified number of millions. How that figure was reached was not explained in detail, although a
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footnote indicates that it was based on the number of unknown DNA sequences found in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
environmental samples. Second, a critical survey of world species numbers by Chapman (2009) accepted the 1.5 million figure for the world's fungi. More recently, Scheffers et al. (2012) compiled estimates across all "non-microbial" groups, and discussed the various numbers suggested for fungi, drawing attention to controversial points identified, particularly those associated with scaling. Those authors also stress the need for genomic surveys of the fungi in moist tropical forest soils to facilitate comparison with data from temperate forests. In addressing the issue of missing species of all kinds of organisms, they produce evidence that suggests that most probably live in biodiversity hot-spots.
Evidence from the tropics More extensive data relating to two issues are a particular need in developing more robust estimates of global species numbers of fungi: (1) the numbers of new species to be found in particular tropical sites; and (2) fungus:plant ratios in the tropics at a range of spatial scales. Studies of particular sites in temperate regions show that the number of species of fungi detected macroscopically or microscopically continued to rise for decades, and the rise is on-going. In no site that has been subject to repeated visits, even over 40 years or more, has the species accumulation curve reached an asymptote. Consequently, short-term visits to tropical sites can only be expected to yield a small proportion of the species present. Further, those species that are commonest are most likely already to have been named, while species that are new to science may be rarer, and so are less likely to be detected outside long-term surveys. There are no published results from any long-term studies, in which all the fungi in every ecological niche in a tropical forest have been surveyed. This would be a huge task which would involve numerous mycologists and a variety of methodologies (Rossman et al. 1998, Mueller et al 2004). However, pertinent information can be found in a number of significant compilations (e.g. Isaac et al. 1993, Hyde 1997, Janardhanan 1997, Watling et al. 2002, Deshmukh and Rai 2005), as well as in reviews cited in the previous section. The seven-season study of ectomycorrhizal fungi of Dicymbe legume forest in central Guyana, reported in this issue (Henkel et al. 2012), nevertheless gives some indication of comparability. By combining data from sporocarps and sequence data from ectomycorrhizal roots, those authors concluded that the actual number of these fungi in the area was in
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excess of 250 species – a result comparable to that of studies in boreal and temperate 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
forests. In the course of this and other studies in this region of Guyana, about 750 species of agarics new to science have been discovered (M. C. Aime, in litt.). Of the 632 species of larger fungi encountered in Colombian Amazon forests in the course of 6–7 visits over 3½ years by López-Quintero et al. (2012), 52 % could not be identified to species, and the authors considered that a significant proportion of those represented species new to science. When particular groups of fungi are studied in depth in the tropics, high levels of novelty are generally found. This is illustrated in this issue by the study of mycorrhizal Sebacinales associated with Ericaceae and Orchidaceae in Ecuador, where 74 % of the species were previously undetected and apparently endemic (Setaro et al. 2012). The reverse also applies in some groups, notably the rusts, in which it has long been recognized that the fungus:plant ratios are higher in temperate than tropical regions, a result confirmed for the neotropics by the analysis of Berndt (2012). In contrast, in some other groups of plant-restricted microfungi, new species continue to be described apace from the tropics. A recent example is that of the Meliolales in India, where the number has increased from 378 to 611 (62 %) in just 12 years, mainly due to the work of a single mycologist and his coworkers (Hogasadukar 2008). The lack of comprehensive estimates of fungus:plant ratios in the tropics remains a problem and such studies are vital to the questions posed here. A most valuable indication of the type of study that might be done is that of Piepenbring et al. (2012). Those authors surveyed the numbers of both plants and both macro- and microscopic fungi along a 500 m pathway in Panama monthly over two years. They recorded 567 species of fungi and 311 species of plants, giving a ratio of 1.8: 1. While such a study would need to be conducted for at least two decades to facilitate comparison with the most intensively studied sites in the UK, the total is not dissimilar to what would be expected for a study in such a restricted time frame in that country.
Evidence from non-tropical site inventories Pertinent data on fungus:vascular plant species ratios continue to be accumulated from outside the tropics, both through long-term field recording, and as a result of molecular work. In the case of the now most intensively field-recorded site in the world, Esher
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Common (Surrey, UK), the number of fungal species now stands at about 3500, and that of 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
vascular plants at 420 (B. M. Spooner, pers. comm.); this yields a fungus:plant ratio of 8.2. In a study of boreal forest soils in Alaska, molecular data detected over 1500 fungi compared with fewer than 200 plants (Taylor et al. 2010), suggesting a ratio of 7.5:1 – an underestimate as non-soil samples (e.g. lichen-forming fungi on rocks and trees) were not included, and the molecular data sets were not comprehensive.
Evidence from cryptic species The existence of distinct but morphologically indistinguishable species is one of the places where the 1.4 million plus predicted "missing species" are to be found. Hawksworth & Rossman (1997) suggested that the number of known fungi should perhaps be multiplied "by a factor of five or more" to allow for these "cryptic species". That multiplication factor was based on the synopsis of the numbers of cryptic species reported in 45 well-studied morphospecies prepared by Brasier (1987), which ranged from two to 19. At that time, cryptic species were recognized primarily by incompatibility, but as more and more fungi of diverse taxonomic groups have been studied in depth by molecular methods, it is clear that it is commonplace for specimens or cultures of the same morphologically circumscribed species, to comprise suits of cryptic species. Physiological and other biological speciation events evidently often precede morphological divergence in the evolution of fungal species. Further, cryptic speciation is not restricted to plant pathogens, as might have been anticipated where "special forms" had historically been recognized, but to occur in disparate fungal groups, not least amongst lichen-forming species where there are now numerous cases recognized (Crespo and Lumbsch 2010). Examples across the fungi are numerous, and may be exemplified by the study of Bensch et al. (2010) on over 200 strains that had been named as "Cladosporium cladosporioides"; multi-gene and more critical culture and micromorophological studies resulted in the description of 22 species new to science in this "one" species. Interestingly, after clades have been recognized by molecular phylogenetic methods, it is sometimes possible a posteriori to find correlations with cultural, physiological, or morphological features valuable for the separation of the newly recognized cryptic species. Such investigations are also demonstrating that assumptions of species being widely distributed, even across continents, are often incorrect. Even amongst the macromycetes, where the same scientific name has been applied to morphologically similar
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populations in Europe and North America for 150 years or more, the representatives are 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
being found to belong to different species requiring new names (Petersen and Hughes 2012). In morphologically circumscribed fungal species that have been subjected to intensive molecular phylogenetic studies, there has been no analysis of the numbers of these in which cryptic speciation has been found, or the mean number of cryptic species present. Such a desk-study is required to determine if the five-times correction factor to allow for cryptic species suggested by Hawksworth and Rossman (1997) should be higher or lower.
Evidence from environmental molecular biology Next generation high-throughput sequencing techniques are revealing an astonishing level of fungal species richness. Since 454-sequencing technology started to be used for fungi (Buée et al. 2009, Lentendu et al. 2011), studies are being published which demonstrate the enormous hyper-diversity present in the fungi, especially in soil samples. For example, Taylor et al. (2010) recovered over 5000 high-quality sequences from a 0.25 g soil sample, representing 218 species, from an Alaskan forest. Further, that sample, and one of a similar size collected 1 m away from the first, had only 14 % of the species in common. These authors comment that with current technologies "it is practically impossible to saturate fungal diversity even in miniscule samples". To date, there is little next generation sequencing of fungi from tropical habitats, a notable exception being the study of McGuire et al. (2011) on soil and litter fungi in forest plots in Panama. Contrary to expectations, there was no relationship between fungal species and plant species richness; there was, however, a strong positive correlation between soil fungal richness and increasing precipitation. More recently, Geml et al. (2012) reported on pyrosequencing studies from Yungas forests in the Andes. They found 1,839 species-like taxa of which 25 % were most similar to other unidentified environmental samples and could not be assigned to a phylum, and also that there were significant differences in the taxa present in three different forest types located at different altitudes. Next generation sequencing of fungi from deep sea and other ocean sediments does not appear to have been reported to date, but could yield additional data on the extent of unknown fungal species. The study of such communities by culture methods is complicated
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because of the high atmospheric pressures that need to be maintained to study them, but 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
nevertheless some progress has been made (Raghukumar and Damara 2008). Molecular methods now starting to be applied, however, are revealing a diversity of apparently unnamed fungal species, including a new branch of Chytridiomycota (Le Calvez et al. 2009), although they appear to be relatively rare with yeast-like forms predominating (Bass et al. 2007). The global estimate of 3.5–5.1 million fungal species by O'Brien et al. (2005) was based on the ratio of the numbers of fungi detected by large-scale sequencing of soil from two plots from different parts of one forest, and the number of plant species at each site. One site had 491 fungi and 26 plants, and the other 616 fungi and 48 plants, giving ratios of 19:1 and 13:1, respectively. Extrapolation of those ratios to the global level, based on 270,000 species of plants, yielded the cited numbers. Molecular studies on environmental samples repeatedly yield fungal sequences that do not correspond to any allocated a scientific name in GenBank. This is becoming a major problem, in that while there are 20,765 named fungal species in GenBank, there are a further 43,290 not named to species – and of the latter, 11,429 are not even named to genus (C. L. Schoch, pers. com.). While a proportion of these unnamed sequences will represent some of the 80,000 accepted (but as yet unsequenced) fungal species, perhaps the majority are from taxa yet to be named formally. The desirability of naming taxa only known from environmental sequences, and the manner in which they should be named, is a matter currently under debate (Hibbett et al. 2011). Concerns relate to the requirement for material that can serve as the name-bearing type for the name to be permanently preserved for study by future researchers (which must be a specimen, permanently preserved culture, or illustration under the current Code), what sequence data should be required, and that some will be of already named species not represented in GenBank. It is anticipated that guidance on these matters will be developed by the International Commission on the Taxonomy of Fungi (ICTF) within the next few years.
Global species numbers revisited The evidence now available suggests that there are at least 1.5, but probably as many as 3 million species of fungi on Earth. Studies of fungal diversity during the last two decades have indicated that the 1.5 million global estimate is, indeed, a conservative one as originally
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emphasized (Hawksworth 1991). A decade later, updates of the calculations in that paper, 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
based in particular on revised upward estimates of global vascular plant species numbers, suggested a number of 2.3 million (Hawksworth 2001). The number of fungi recognized in the UK has now risen from around 12,000 in 1990, to over 14,000; about 40 species continue to be added each year. Further, results from the exploration of previously littleresearched ecological niches, such as those within animal guts (Griffith et al. 2010) and within rocks (Ruibal et al. 2009), have yielded previously unsuspected high levels of fungal diversity. Unfortunately, little progress has been made in developing improved estimates of the extent of insect-associated fungi in recent years. These remain largely ignored in extrapolations of species richness at the global scale. Taking these into account could be expected to result in an overall increase in estimates of species numbers worldwide; the range of fungus-insect interactions is enormous (Vega and Blackwell 2005), but the degree of host specialization is in most cases as yet unclear. A conservative lower estimate of the numbers of fungal species, 712,000, was arrived at by Schmit and Mueller (2007), and the consensus amongst mycologists today, is that the 1.5 million estimate is excessively restrained. However, while there is no agreement on a likely upper figure, there is increasing support for the view that the magnitude of the actual number is in millions. In order to make further progress, there are two principle issues that need to be resolved. First, the validity of extrapolating fungus:vascular plant ratios from local or national studies to the global scale. With respect to ratios, it is also sometimes not appreciated that the numbers of fungi in all habitats were considered when deriving the 6:1 ratio, and not just those directly associated with vascular plants (Hawksworth 1991). Further, it was also recognized at that time that the ratio would be vastly greater in the case of regions with relatively few plant species, such as the antarctic, boreal forests, tundra, and hot-deserts. Recognizing the difficulties of undertaking long-term surveys over decades, and the practical difficulties of determining the fungi present in all habitats in a site, including soil, lichenforming fungi, endophytic fungi, those in and on insects and other arthropods, there could be value in using a standardized survey protocol from the tropics to the arctic. One option to consider is a series of “extensive surveys” in different biomes using the same survey methods. These could then be calibrated with a limited number of sites where ”intensive surveys” had been, and are continuing to be, conducted (Hawksworth et al. 1997).
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Second, the extent to which many of the environmental sequences being discovered, 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
many of which appear to represent hitherto unnamed fungi and even fungal lineages, are restricted by host, climatic factors, or geography. In addition, to date, next-generation sequencing has tended to focus on soil samples in a site and not all the potential fungal habitats present in a locality. The extent to which the numbers of fungi found in soil samples are a reflection of the total actually present in a site is currently uncertain. The predictive power of next generation sequencing needs to be ascertained is clarified as to the relationship between data from minute soil samples and the fungi known to be present in a site from macro- and microscopical studies is unclear. Notwithstanding the above caveats, data emerging from tropical studies and, in particular, environmental and phylogenetic molecular investigations, indicates that 1.5 million is indeed a low estimate of the number of fungal species worldwide. However, it has to be recognised that it is unlikely that sufficient data will be available for many years that could allow the calculation of a number in which there may be more confidence. This is inevitable in view of the magnitude of the tasks, and the limited numbers of mycologists engaged in systematic and ecological studies. This is a particular problem in the tropics; information from long-term, intensive fungal inventories is acutely needed in these regions, and will be critical in assessing the predictive power of sequencing studies on soil samples from tropical sites. Unfortunately, inventory studies over periods of many years are not easily accommodated into the funding framework models of most grant-awarding bodies. I feel it is important that the global biodiversity and conservation science communities, ecologists, and the public at large, are given an indication of the extent of the vast unexplored fungal world. At the same time, it is unhelpful for a discipline to be seen to have widely varying figures promulgated, even if that is done with sound intentions. Repeated switches tend to be taken as indications of uncertainty which, while they may be justifiable scientifically, may give the impression of a field in chaos rather than a discipline progressing in a confident manner. The 1.5 million figure, although put forward as an hypothesis for testing, has become widely used and cited in scientific and semi-popular arenas; indeed, a search in Google for "1.5 million species fungi" yielding 2,650,000 hits in June 2012. As we still lack evidence to be confident as to how many millions may be a more likely estimate, for the present, it is perhaps most appropriate to use a phrase such as "at least 1.5, but probably as many as 3 million". It appears prudent to refrain from inflating the
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figures further until there is greater certainty over the validity of extrapolations used by 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
various authors in reaching their estimates. In particular, we still know very little of the geographical distribution of unidentified sequences and large-scale patterns of fungal distributions. Over-emphasis of results from the limited number of available data-sets is to be avoided as potentially misleading in our current state of knowledge.
Acknowledgements M. Catherine Aime, Conrad L. Schoch, and Brian M. Spooner are thanked for providing previously unpublished data, three referees and the Editors for making several constructive suggestions, and my wife, Patricia E. J. Wiltshire-Hawksworth, for improving the clarity of my draft and for critical comments. This work was undertaken while in receipt of funding from the Ministerio de Economía y Competitividad of Spain under project CGL2011-25003.
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