http://orcid.org/0000-0002-1235-4418
Figures
Abstract
The Amazon Forest is a hotspot of biodiversity harboring an unknown number of undescribed taxa. Inventory studies are urgent, mainly in the areas most endangered by human activities such as extensive dam construction, where species could be in risk of extinction before being described and named. In 2015, intensive studies performed in a few locations in the Brazilian Amazon rainforest revealed three new species of the genus Scleroderma: S. anomalosporum, S. camassuense and S. duckei. The two first species were located in one of the many areas flooded by construction of hydroelectric dams throughout the Amazon; and the third in the Reserva Florestal Adolpho Ducke, a protected reverse by the INPA. The species were identified through morphology and molecular analyses of barcoding sequences (Internal Transcribed Spacer nrDNA). Scleroderma anomalosporum is characterized mainly by the smooth spores under LM in mature basidiomata (under SEM with small, unevenly distributed granules, a characteristic not observed in other species of the genus), the large size of the basidiomata, up to 120 mm diameter, and the stelliform dehiscence; S. camassuense mainly by the irregular to stellate dehiscence, the subreticulated spores and the bright sulfur-yellow colour, and Scleroderma duckei mainly by the verrucose exoperidium, stelliform dehiscence, and verrucose spores. Description, illustration and affinities with other species of the genus are provided.
Citation: Baseia IG, Silva BDB, Ishikawa NK, Soares JVC, França IF, Ushijima S, et al. (2016) Discovery or Extinction of New Scleroderma Species in Amazonia? PLoS ONE 11(12): e0167879. https://doi.org/10.1371/journal.pone.0167879
Editor: Jae-Hyuk Yu, University of Wisconsin Madison, UNITED STATES
Received: September 27, 2016; Accepted: November 15, 2016; Published: December 21, 2016
Copyright: © 2016 Baseia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper.
Funding: We are grateful to the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq—Brazil, process PVE/407474/2013-7 and PPBio/457476/2012-5), and Fundação de Amparo à Pesquisas do Estado do Amazonas (FAPEAM-Brazil) for the financial support; as well as to Centro de Estudos Integrados da Biodiversidade Amazônica.
Competing interests: The authors have declared that no competing interests exist.
Introduction
Amazonia is the largest and most diverse of the world’s tropical rainforests, encompassing more than 6 million km2 in nine countries of South America. According to the Rainforest Conservation Fund [1], in the rainforest most of the organisms are undescribed and unknown. Recent studies indicate at least 427 amphibians, 1294 birds, 3,000 fishes, 378 reptiles, 427 mammals, and 40,000 plant species in Amazonian rainforest [2]. Studies on fungi from the Brazilian Amazon forest have reported about 1000 species of macrofungi [3]. Knowledge of fungal diversity is amplified through advances in laboratory methodologies and computational analysis [4,5]. Molecular studies combined with morphological knowledge has led to a better delimitation of taxonomic groups, determining which morphological characters are informative, or not, so as to detect cryptic species. On the other hand, there seems to be consensus that these rainforests are reservoirs of the greatest amount of biodiversity as yet uncatalogued by science [6,7,8], which makes the destruction of the tropical rainforests the main challenge facing the discovery of fungi that are still unknown.
To ensure energy independence and exploit mineral resources, the governments of Amazonian countries are embarking on a major dam building drive on the basin’s rivers, with 191 dams finished and a further 246 planned or under construction. This rush to reap the basin’s renewable energy has come without considering the negative environmental consequences to the most speciose freshwater and terrestrial biomes of the world [9].
Brazil has emerged as one of the few countries where deforestation is falling, due to programs aimed at protecting forest areas such as blacklisting on deforestation. Critical districts with high annual forest loss are included in blacklists published regularly by the Brazilian Ministry of the Environment, and farms in those blacklists face new administrative rules to obtain licenses for clearing forests. This practice contributed to reducing the average deforestation in the years 2002 to 2012 [10,11]. Extensive projects on biodiversity studies were implemented and helped to demarcate, justify and maintain biological reserves across the country, for example, the Research Program on Biodiversity (PPBio) and the Integrated Studies Center of the Amazonian Biodiversity (CENBAM). However, the construction of increasing numbers of hydroelectric dams throughout the Amazon has led to destruction and irreversible ecological imbalance in many areas [12,13,14].
The diversity of macrofungi species present in the tropical rainforest is still insufficiently known, and Hawksworth [7] considers this biome the largest reserve of biodiversity on the planet. So far, only around 1000 species of macrofungi have been described for the Amazon forests [3]. For gasteroid fungi, 20 species have been described distributed in the states of Amazônia, Pará and Rondônia [15,16,17,18,19,20,21].
The genus Scleroderma was described in 1801 by Persoon and is currently included in the order Boletales [22]. In accordance with Guzmán et al. [23], Scleroderma is divided into three sections based on the surface structure of the basidiospores and on the presence or absence of a clamp connection: (1) Reticulatae, characterized by reticulated spores, (2) Scleroderma, with echinulate spores, and (3) Sclerangium, presenting subreticulated spores. Molecular studies, based on comparison of Internal Transcribed Spacer (ITS) nrDNA, confirm this classification [24,25].
This genus is distributed in tropical, subtropical and temperate regions, forming ectomycorrhizas [26]. In Brazil, there is a register of 15 species [17,27,28,29,30,31,32,33,34,35,36,37,38,39]. All of these registers were observed in exotic vegetation (Pinus spp, Eucalyptus spp, etc.), with the exception of S. minutisporum Baseia, Alfredo & Cortez and S. dunensis BDB Silva, Sulzbacher, Grebenc, Baseia & MP Martín, which were found in native vegetation of the Amazon rainforest [17,39]. Scleroderma tenerum Berk & M.A. Curtis, and S. tuberoideum Speg. are considered synonymous with S. nitidum Berk. and S. albidum Pat. & Trab., respectively [23,30].
On March 28, 2015, some of the authors of this article (NKI, IFF, SU and NM) visited Camassú, one of about 50 islands that would be flooded due to construction of Belo Monte Dam; they collected a number of Scleroderma specimens that were not possible to assign to any known species.
This work describes novelties of the genus Scleroderma from the Amazon rainforest with analyses based on morphological and molecular data.
Material and Methods
Collections studied
The species were collected from native vegetation of the Brazilian Amazon rainforest, and were deposited in Brazilian and Spanish collections: UFRN (Rio Grande do Norte), INPA (Amazonas) and MA-Fungi (Madrid). Data of collections studied are included in Table 1. All necessary permits were obtained for studies issued by the Curators of the Herbaria (reference document number UFRN-02/2015, INPA-13/2015).
(n.d.: no data). In bold, new species described in this study.
Morphological analysis
The morphological analyzes with dry material followed preliminary studies [23,30,40,41,42,43], and were performed in the fungal biology laboratory at the Universidade Federal do Rio Grande do Norte. Measurements were performed using a ruler attached to the microscope with smallest divisions at 1 mm. For microscopic analysis hand-cut sections of the layers of the peridium and spores, mounted in 5% KOH, Melzer's reagent and Congo Red were examined with the light microscope. The standardization of the colors followed Kornerup and Wanscher [44].
Molecular analyses
Samples for DNA extraction were excised from dry basidiomes. To avoid contamination by other fungi, pseudotissues were taken from the inner part of the basidiome. DNA extraction, amplification, and sequencing of the ITS regions including the 5.8S of the ribosomal RNA gene cluster followed the protocols mentioned by Phosri et al. [24]. The ITS regions were amplified with Ready-To-GoTM PCR Beads (GE healthcare Life Sciences, NJ, USA), using the primers ITS1F [45] and ITS4 [46], and the cycling protocol described in Martín and Winka [47]. Aliquots of the purified products were mixed separately with the direct and reverse primers before sending them to Macrogen (South Korea) for sequencing. Consensus sequences were assembled using Sequencher software (Gene Codes Corporation Inc, Ann Arbor, Michigan, USA). Previous to the alignment, sequences were compared with homologous sequences from the EMBL/GenBank/DDBJ [48] using the BLASTn algorithm [49]. All new sequences have been deposited on the EMBL-EBI database and their accession numbers are presented in Table 1.
Using SEQAPP software (PerkinElmer Applied Biosystems), multiple sequence alignments were performed of the consensus sequences obtained in this study and homologous sequences from the EMBL/GenBank/DDBJ, (http://www.ncbi.nlm.nih.gov/entrez/) (Phosri et al. [24], Rusevska et al. [25], and Crous et al. [39]) shown in Table 1. The alignment was optimized visually. Alignment gaps were indicated as “-” and ambiguous nucleotides were marked as “N”.
The alignment was analyzed using the programms PAUP 4.0a147 [50], MrBAYES 3.2.2 [51] and RAxML [52] using the CIPRES portal (http://www.phylo.org/portal2/) [53]. Pisolithus arhizus FM213365 was used as outgroup, since this species is closely related to Scleroderma [54]. First, a parsimony analysis under a heuristic search was conducted. Gaps were treated as missing data. The tree branch robustness was estimated by bootstrap (MP-BS) analysis [55] employing 10000 replicates, using the fast-step option. The starting branch lengths were obtained using the Roger-Swofford approximation method and the starting trees for branch swapping were obtained by stepwise addition. The tree bisection-reconnection (TBR) branch-swapping algorithm was used with the Multitrees options. The data were further analyzed using a Bayesian approach [56,57]. The posterior probabilities (PP) were approximated by sampling trees using the MCMC method. The Bayesian analysis was performed assuming the general time reversible model [58] including estimation of invariant sites and assuming a discrete gamma distribution with six rate categories (GTR+I+G). A run with 2M generation starting with a random tree and employing 12 simultaneous chains was executed. Every 100th tree was saved into a file. The log-likelihood scores of sample points were plotted against the number of generations using TRACER 1.0 (http://evolve.zoo.ox.ac.uk/software.html) to determine that stationarity was achieved when the log-likelihood values of the sample points reached a stable equilibrium value [51]. The initial 1000 trees were discarded as a burn-in before calculating posterior probabilities (PP). Using the “sumt” command of MrBAYES, the majority-rule consensus tree was calculated from 19K trees sampled after reaching likelihood convergence to calculate the posterior probabilities. A third maximum likelihood bootstrapping analysis was performed with RAxML 7.2.8 [52], using the default parameters as implemented on the CIPRES NSF XSEDE resource with bootstrap statistics calculated from 1000 bootstrap replicates (ML-BS) under GTR + I + G model of evolution.
The phylogenetic tree was drawn with the program TreeView [59] and edited in Adobe Illustrator CS3; names of clades and subclades are according to Phosri et al. [24], Rusevska et al. [25], and Crous et al. [39]. A combination of MP-BS, ML-BS, and PP was used to assess confidence for a specific node [60,61].
Nomenclature
The electronic version of this article in Portable Document Format (PDF) in a work with an ISSN or ISBN will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic publication of a PLOS ONE article are effectively published under that Code from the electronic edition alone, so there is no longer any need to provide printed copies.
In addition, new names contained in this work have been submitted to MycoBank, from where they will be made available to the Global Names Index. The unique MycoBank number can be resolved and the associated information viewed through any standard web browser by appending the MycoBank number contained in this publication to the prefix at http://www.mycobank.org/MB. The online version of this work is archived and available from the following digital repositories: PubMed Central, LOCKSS and Digital-CSIC.
Results
Molecular studies
The sequences obtained from Amazonian specimens have been deposited within EMBL (http://www.ebi.ac.uk/embl) with the accession numbers indicated in Table 1. The topologies of the three analyses performed (Maximum parsimony, Maximum likelihood and Bayesian) were similar to each other; the 50% majority-rule consensus tree from the Bayesian analysis is shown in Fig 1 with MP-BS, ML-BS and PP on branches. At least 20 clades can be assigned to Scleroderma species already defined in Crous et al. [39]. As indicated in Fig 1, the Amazonian specimens grouped into three different clades.
Numbers above branches are parsimony bootstrap (MP-BS), maximum likelihood bootstrap (ML-BS) and posterior probability (PP) values. The position of the three new species described in this paper are marked in colours, indicated by the herbarium number (UFRN = UFRN-Fungos); the rest of branches indicated with their respective GenBank accession numbers, indicated in Table 1.
The sequence from collection UFRN-Fungos 2790 is the sister group of the clade formed by Scleroderma sinnamariense Mont. and S. xanthochroum Watling & K.P. Sims. This relationship is very well supported (MP-BS = 74%, ML-BS = 99%, PP = 1.0); although, the specimens of collection UFRN-Fungos 2790 show unusual spore ornamentation for a Scleroderma: small granules under SEM; whereas in S. sinnamariense spores are echinulate and in S. xanthochroum reticulated [62].
The rest of the specimens grouped together with low MP-BS support (< 50%), although distributed in two different clades. One clade contained the two collections UFRN-Fungos 2794 and UFRN-Fungos 2795 with significant support (MP-BS = 100%, ML-BS = 100%, PP = 1.0); these collections are from the Reserva Florestal Adolfo Duke, and the specimens show spores slightly spiny under LM. In the other clade, the collections INPA 271114 and UFRN-Fungos 2792, grouped together, with low MP-BS support (< 50%), and strong ML-BS (90%) and PP (0.98); the number of differences between the sequences of these collections (Fig 1) suggests to us that they could belong to two different taxa, but specimen UFRN-Fungos 2792 was not in good enough condition to perform a complete morphological analysis.
Based on morphological and molecular analyses, S. anomalosporum (UFRN-Fungos 2790), S. camassuense (UFRN-Fungos 2793), and S. duckei (UFRN-Fungos 2794 and UFRN-Fungos 2795) are proposed as new species.
Taxonomy
Scleroderma anomalosporum Baseia, B.D.B. Silva & M.P. Martín sp. nov., Mycobank MB 818095
Etymology. In reference to unusual spores compared to the pattern of spores of the genus Scleroderma.
Holotype. Brasil, Pará, Altamira, Ilha Camassú, S03°16'46.0" W052°12'17.1", 28 Mar. 2015, leg. N.K. Ishikawa & I.F. França (UFRN-Fungos 2790; ITS nrDNA sequence Acc. Number KX792084).
Isotypes. INPA 271001; MA-Fungi 89305
Diagnosis. Basidiomata epigeous, sessile, opening by stellate dehiscence, up to 115 mm diam, surface reticulated. Peridium 450–600 mm thick, consisting of three layers. Gleba when mature protected by the inner layer of peridium. Basidiospores 3.5–5.3 × 3.8–5.4 μm diam, globose to subglobose, smooth under LM, with small granules on the surface under SEM.
Description. Basidiomata epigeous, sessile, subglobose when closed, up to 90 mm diam × 45 mm high; when mature, stellate dehiscence forming 5–7 irregular branches, the expanded basidiomata up to 115 mm diam × 75 mm high, with rhizomorphs aggregated at the base (Fig 2A). Surface reticulated, brown (5F6, 5F7) to dark brown (6F6) at maturity, with aggregated soil particles (Fig 2B). Peridium 450–600 mm thick, with three layers (Fig 2C): the outer layer made of cylindrical hyphae, yellowish in KOH, 2.5–6.5 μm diam, walls up to 1.0 μm thick, winding (Fig 2D); the middle layer consists of cylindrical hyphae, with rounded ends at the surface, hyaline in KOH, 4.5–16 μm diam, walls up to 2.5 μm thick; and inner layer pale yellow (3A3), composed of interwoven cylindrical hyphae, hyaline in KOH, 4.0–6.5 μm diam, walls up to 1.0 μm thick, clamp connections rare. Gleba when mature greyish brown (6E3), compact to powdery at maturity, protected by the inner layer of peridium. Basidiospores 3.5–5.3 × 3.8–5.4 μm diam including ornamentation, globose to subglobose, hyaline to yellowish in KOH, smooth under LM (Fig 2E), with small granules on the surface under SEM (Fig 2F).
(A) Fresh basidiomata in the field, bar = 30 mm. (B) Detail of reticulation in exoperidium of young basidioma, bar = 2 mm. (C) Basidioma cut away side view, bar = 2 mm. (D) Exoperidium hyphae, bar = 20 μm. (E) Basidiospores under LM, bar = 10 μm. (F) Basidiospores under SEM, bar = 2 μm.
Remarks. Scleroderma anomalosporum is characterized mainly by the smooth spores under LM in mature basidiomata and the large size of the basidiomata, being capable of achieving up to 120 mm in diameter when expanded, and the stelliform dehiscence. In accordance with Guzmán et al. [22], smooth spores in the genus Scleroderma are found in immature basidiomes, and when mature, the spores vary between reticulated, subreticulated and echinulate. The spores of S. anomalosporum under SEM present small, unevenly distributed granules, a characteristic not observed in other species of the genus. Scleroderma polyrhizum (J.F. Gmel) Pers. and S. texense Berk. present basidiomata that can reach up to 150 mm and 140 mm, respectively, when expanded. However, they have larger spores (7–11 μm in diameter) than S. anomalosporum, and different ornamentation: subreticulated and lightly echinulate spores in S. polyrhizum [23,30], and reticulated in S. texense [23,30].
Scleroderma camassuense M.P. Martín, Baseia & B.D.B. Silva sp. nov., Mycobank MB 818096
Etymology. In reference to the type locality in the state of the Pará.
Holotype. Brasil, Pará, Altamira, Ilha Camassú, S03°16'46.0" W52°12'17.1", 28 Mar. 2015, leg. N.K. Ishikawa & I.F. França (UFRN-Fungos 2793, ITS nrDNA sequence Acc. Number KX792085).
Isotype. INPA 271114
Diagnosis. Basidiomata epigeous, sessile or pseudostipitate, opening by a dehiscence irregular to stellate, up to 20 mm diam, surface scaly to verruculose. Peridium up to 0.5 mm thick, consisting of three layers. Basidiospores 6.4–8.0 × 5.6–7.5 μm diam, globose to subglobose, subreticulated under LM, irregular reticulum under SEM.
Description. Basidiomata epigeous, sessile or pseudostipitate, globose to subglobose when closed, up to 14 mm diam × 12 mm high; when mature, irregular to stellate dehiscence forming 4–6 irregular branches, expanded up to 20 mm diam × 11 mm high (Fig 3A). Generally, there are yellow (2A6) rhizomorphs or mycelium attached at the base (Fig 3B). Surface scaly to verruculose, dark brown (6F4) at maturity, with soil particles aggregated (Fig 3B). Peridium 0.5 mm thick, consisting of three layers (Fig 3C); the outer layer made of oleoacanthohyphae with yellowish contents in KOH, 5.5–10.5 μm diam, walls up to 1.0 mm thick (Fig 3D); the middle layer sulphur yellow (1A5), composed of interwoven cylindrical hyphae, hyaline in KOH, 3.5–6 μm diam, walls up to 1 μm thick; and the inner layer sulphur yellow (1A5), composed of pseudoparenchymatous cells, hyaline in KOH, 26–57 × 13–35.5 μm, walls up to 1 mm thick. Gleba when mature brown (5E4) to greyish brown (6F3), compact to powdery at maturity. Basidiospores 6.4–8.0 × 5.6–7.5 μm diam including ornamentation, globose to subglobose, brownish in KOH, subreticulated under LM (Fig 3E), irregular reticulum under SEM (Fig 3F).
(A) Fresh basidiomata in the field, bar = 10 mm. (B) Detail of verrucose exoperidium surface, bar = 2 mm. (C) Basidioma cut away side view, bar = 2 mm. (D) Exoperidium hyphae, bar = 20 μm. (E) Basidiospores under LM, bar = 10 μm. (F) Basidiospores under SEM, bar = 2 μm.
Remarks. Scleroderma camassuense is characterized mainly by the irregular to stellate dehiscence, the subreticulated spores and the yellow sulfur colour. Scleroderma sinnamariense, S. verrucosum (Bull.) Pers., S. citrinum Pers. and S. uruguayense (Guzmán) Guzmán also present a dark yellow peridium, but can be distinguished by the size of the larger basidiomata (up to 45 mm in diameter) and the presence of pilocystidia in the external layer of the peridium in S. sinnamariense [30,42]; by the larger and echinulate spores (9–12 μm in diameter) in S. verrucosum [43]; and by the larger and reticulated spores (11–14 μm in diameter) in S. citrinum and S. uruguayense [30,43].
Subreticulated spores and stellate dehiscence are also observed in Scleroderma bermudense Coker, S. floridanum Guzmán, S. stellatum Berk., S. polyrhizum and S. texense. However, they can be differentiated from one another by the larger basidiomata (up to 34 mm in diameter), whitish or light brown peridium, and presence of interlaced fibrils in S. bermudense [43]; by the larger spores (8.8)10.4–13.6(–16) μm and flaky surface of the exoperidium in S. floridanum [29]; by the echinulate exoperidium in S. stellatum [43]; by the larger spores (6)7.2–9.6(–12) μm and larger basidiomata in S. polyrhizum and S. texense with 140 mm and 150 mm, respectively [23,30].
Scleroderma duckei B.D.B. Silva, M.P. Martín & Baseia sp. nov., Mycobank MB 818097
Etymology. In reference to the type locality, Reserva Florestal Adolpho Ducke
Holotype. Brasil, Amazonas, Manaus, Reserva Adolpho Ducke, S02°57'37.3" W59°55'55.1", 21 Mar. 2015, leg. N.K. Ishikawa & J.V.C. Soares (UFRN-Fungos 2794, ITS nrDNA sequence KX792086).
Isotype. INPA 272127.
Diagnosis. Basidiomata epigeous, sessile, opening by a small stellate dehiscence, up to 25 mm diam, surface verrucose. Peridium up to 0.5 mm thick, consisting of three layers. Basidiospores 5.7–7.1 × 5.7–7.0 μm diam, globose to subglobose, slightly spiny under LM, regularly grouped warts under SEM.
Description. Basidiomata epigeous, sessile, when closed globose to subglobose, up to 20 mm diam × 8 mm high; when mature, small stellate dehiscence that form 5–6 irregular branches, expanded up to 25 mm diam x 16 mm high, with rhizomorphs aggregated at the base (Fig 4A). Surface verrucose, dark brown (6F6, 6F4) at maturity, with aggregated soil particles (Fig 4B). Peridium up to 0.5 mm thick, consisting of three layers (Fig 4C): the outer layer is composed of pseudoparenchymatous irregular cells, yellowish in KOH, 13.5–47.5 × 13–22 μm, walls up to 2.0 μm thick (Fig 4D); the middle layer consists of cylindrical hyphae, clamp connections rare, hyaline in KOH, 5–20 μm diam, walls up to 1.9 μm thick; and the inner layer composed of interwoven cylindrical hyphae, hyaline in KOH, 5–15 μm diam, walls less than 1 μm thick, with clamp connections. Gleba when mature dark brown (7F4), compact to powdery at maturity. Basidiospores 5.7–7.1 × 5.7–7.0 μm diam including ornamentation, globose to subglobose, brownish in KOH, slightly spiny under LM (Fig 4E), regularly grouped warts under SEM (Fig 4F).
(A) Fresh basidiomata in the field, bar = 20 mm. (B) Detail of verrucose exoperidium surface, bar = 2 mm. (C) Basidioma cut away side view, bar = 2 mm. (D) Exoperidium hyphae, bar = 20 μm. (E) Basidiospores under LM, bar = 10 μm. (F) Basidiospores under SEM, bar = 2 μm.
Other material studied. Brasil, Amazonas, Manaus, Reserva Adolpho Ducke S02°57'37.3" W59°55'55.1", 21 Mar. 2015, N.K Ishikawa & J.V.C. Soares (UFRN-Fungos 2795 ITS nrDNA Acc. Number KX792087).
Remarks. Scleroderma duckei is characterized mainly by the verrucose exoperidium, stelliform dehiscence, and verrucose spores, with warts regularly grouped on the surface of the wall and with small spines visible in optical microscopy. Scleroderma bermudense, S. minutisporum, S. sinnamariense. and S. stellatum also present small spores, 5–10 μm [42], 4–7 μm [16], 7–9 μm [42], and (5–)6-7(–9) μm [43], respectively. However, they differentiate themselves from one another by the whitish, light brown or light grey peridium and the presence of interlaced fibrils in S. bermudense [43]; by the spores with an irregular reticule and velutinous or woodruff exoperidium in S. minutisporum [17]; by the sulfur-yellow peridium and spores with well-developed reticule in S. sinnamariense [42]; and by the larger basidiomata (up to 45 mm when expanded), echinulate peridium surface and spores forming a subreticule in S. stellatum [43].
Discussion
The centers of endemism in Amazonia are well established for animals (vertebrates) and plants [63], and the type locality of the two new Scleroderma species, S. anomalosporum and S. camassuense, are within these areas of high endemism. According to Haffer [64], there are many hypotheses proposed to explain barrier formation separating populations and causing the differentiation of species in Amazonia during the course of geological history based on different factors. Among them there is the river hypotheses, due to the barrier effect of Amazonian rivers. Several anthropogenic activities such as accelerated deforestation and flooded areas from the construction of dams, contribute to the rapid habitat degradation in the Central Amazon. These events, and the disorderly growth of cities in Northern Brazil, in association with climate changes, makes the scientific community recognize the urgency in learning about the biodiversity in this kind of megadiverse area, before the current species become extinct due to human activities [65,66,67,68,69].
The results obtained through the morphological and molecular studies show an interesting species richness of Scleroderma with peculiar morphology, as in the case of S. anomalosporum that presents unusual spores in comparison with other species of this genus. The sequences obtained from Amazonian specimens as indicated in Fig 1, show that the Amazonian specimens are grouped in three different clades and well-supported to be considered independent taxa. Scleroderma anomalosporum and S. camassuense are described from Camassú island (type locality) that is now under the unnatural level of the Xingu River waters; and the third new species, S. duckei, is described from a protected reserve by the INPA. After decades of collecting in rainforests, these three species have not been described before, and they could be endemic to their respective habitats. In a recent study of diversity and distribution of ectomycorrhizal fungi in white-sand forests in Amazonia (along the Cuieiras river) and French Guiana [70], only S. minutisporum [17] is mentioned. In Amazonia, species have restricted distribution [71], being very sensitive to any changes in their habitats [72,73]. Based on complete checklists of published flora data from Brazil (Ducke Reserva), French Guiana (Saül region) and Peru (the Iguits area), Hopkins [74] pointed that it is extremely rare to found a species in any locality; based on this, authors claim that the conservation of Amazonian biodiversity requires actions in all landscapes, not only in protected areas [75].
There are enormous shortfalls in biological knowledge of the Amazon rainforest [76]. Although great efforts to develop international research networks are gathering existing data about species diversity, the number of species that the Amazonia contains it is not yet known [77]. With the exiting data, how can we best protect Amazonia’s biodiversity? Authors agree that the more knowledge we have, the better prepared we will be to protect and maintain the Amazonian biodiversity [75]. However, the scientific process of describing new species is slow compared with the high rates of destructions of natural landscapes [75]. At least, two of the species here described, Scleroderma anomalosporum and S. camassuense could already be extinct, since their collections sites are now under water.
What do we already know about fungal extinctions and how much does it matter? When looking through public databases for studies related to fungus (or fungi) and extinction, almost all papers listed concern pathogenic fungi associated, for example, with the risk of extinction and decline of amphibians [78,79], bees [80], bats [81,82,83], or with recent hypotheses about their role in mass extinction of dinosaurs [84], also some related to invasive plants diseases [85]. However, the information related to the extinction of fungi per se is limited [86]. It is well known that fungi play a key role in all biomes as organic matter decomposers and, the great contribution that ectomycorrhizal fungi make to plant nutrition in infertile soils [87], such as Scleroderma species. Many Scleroderma species found in Brazil forms ectomycorrhiza with introduced Pinus spp. and Eucalyptus spp.; however, two species where located in native vegetation of the Amazon rainforest [17,39], as well as, the three species described here. The extinction of any mycorrhizal fungi can be a very important matter to the associate plant.
Our results support the designation of the Amazon Forest as a hotspot [88] with high diversity and several taxa still unknown to Science. Inventory studies are urgent, mainly in the areas most endangered by human activities, where species could be in risk of extinction before being described and named.
Acknowledgments
We are grateful to the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq—Brazil, process PVE/407474/2013-7 and PPBio/457476/2012-5), and Fundação de Amparo à Pesquisas do Estado do Amazonas (FAPEAM-Brazil) for the financial support; as well as to Centro de Estudos Integrados da Biodiversidade Amazônica (INCT-CENBAM). We are extremely grateful to all residents of the communities visited along the rivers of the Amazon basin, who supported us on field trips. To Ruby Vargas-Isla and Mariana R. Mesquita (INPA, Manaus, Brazil) for support in INPA-Herbarium. To Marian Glenn (Seton Hall University, New Jersey, USA) for kindly English revision. We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions.
Author Contributions
- Conceptualization: BDBS MPM NKI IGB.
- Data curation: MPM BDBS IGB.
- Formal analysis: BDBS IGB MPM NKI.
- Funding acquisition: IGB NKI MPM SU NM.
- Investigation: IGB BDBS MPM NKI.
- Methodology: BDBS MPM NKI IGB.
- Project administration: NKI IFF JCVS NM SU.
- Resources: MPM NKI IGB JVCS IFF NM SU.
- Software: MPM BDBS IGB.
- Supervision: IGB NKI MPM.
- Validation: IGB MPM.
- Visualization: MPM BDBS IGB NKI.
- Writing – original draft: IGB BDBS NKI MPM.
- Writing – review & editing: MPM IGB BDBS NKI.
References
- 1.
Rainforest Conservation Fund. 2016 Nov 8. Available from http://www.rainforestconservation.org/rainforest-primer/2-biodiversity/b-how-much-biodiversity-is-found-in-tropical-rainforests/
- 2.
Mittermeier R, Pilgrim J, Rylands AB, Gascon G, Fonseca GAB, Silva JMC, et al. Amazonia. In: Mittermeier RA, Mittermeier CG, Gil PR, Pilgrim J, da Fonseca GAB, Brooks T, Konstant WR. Wilderness: Earth’s last wild places. CEMEX, Agrupacion Serra Madre, S.C., Mexico. 2002; pp. 56–107.
- 3. Maia LC, Carvalho-Júnior AA, Andrade LHC, Gugliotta AM, Drechsler-Santos ER, Santiago ALCMA, et al. Diversity of Brazilian Fungi. Rodriguésia. 2015;66(4): 1033–1045.
- 4. Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH, Kõljalg U. Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective. PLoS ONE. 2006;1: e59. pmid:17183689
- 5. Blackwell M. The fungi: 1, 2, 3. 5.1 million species? Am J Bot. 2011;98: 426–438. pmid:21613136
- 6. Hawksworth DL, Rossman AY. Where are the undescribed fungi? Phytopathology. 1997;87: 888–891. pmid:18945058
- 7. Hawksworth DL. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res. 2001;105(12): 1422–1432.
- 8. Hyde KD. Where are the missing fungi? Does Hong Kong have any answers? Mycol Res. 2001;105: 1514–1518.
- 9. Lees AC, Peres CA, Fearnside PM, Schneider M, Zuanon JAS. Hydropower and the future of Amazonian biodiversity. Biodivers Conserv. 2016;25: 451.
- 10. Hansen MC, Potapov PV, Moore R, Hancher M, Turubanova SA, Tyukavina A, et al. High-Resolution Global Maps of 21st-Century Forest Cover Change. Science. 2013;342 (6160): 850–853. pmid:24233722
- 11. Cisneros E, Zhou SL, Börner J. Naming and Shaming for Conservation: Evidence from the Brazilian Amazon. PLoS ONE. 2015;10(9): e0136402. pmid:26398096
- 12. Pringle CM, Freeman MC, Freeman BJ. Regional effects of hydrologic alterations on riverine macrobiota in the New World: tropical-temperate comparisons. BioScience. 2000;50: 807–823.
- 13. Finer M, Jenkins CN. Proliferation of Hydroelectric Dams in the Andean Amazon and Implications for Andes-Amazon Connectivity. PLoS ONE. 2012;7(4): e35126. pmid:22529979
- 14. Kahn JR, Freitas CE, Petrere M. False Shades of Green: The Case of Brazilian Amazonian Hydropower. Energies. 2014;7: 6063–6082.
- 15. Trierveiler-Pereira L, Gomes-Silva AC, Baseia IG. Notes on gasteroid fungi of the Brazilian Amazon rainforest. Mycotaxon. 2009;110: 73–80.
- 16. Leite AG, Assis HK, Silva BDB, Sotão HMP, Baseia IG. Geastrum species from the Amazon Forest, Brazil. Mycotaxon. 2011;118: 383–392.
- 17. Alfredo DS, Leite AG, Braga-Neto R, Cortez VG, Baseia IG. Scleroderma minutisporum, a new earthball from the Amazon rainforest. Mycosphere. 2012a; 3(3): 294–299.
- 18. Alfredo DS, Leite AG, Braga-Neto R, Baseia IG. Two new Morganella species from the Brazilian Amazon rainforest. Mycosphere. 2012b;3: 66–71.
- 19. Silva BDB, Cabral TS, Marinho P, Ishikawa NK, Baseia IG. Two new species of Geastrum (Geastraceae, Basidiomycota) found in Brazil. Nova Hedwigia. 2013; 96(3–4): 445–456.
- 20. Cabral TS, Silva BDB, Ishikawa NK, Alfredo DS, Braga-Neto R, Clement CR, et al. A new species and new records of gasteroid fungi (Basidiomycota) from Central Amazonia, Brazil. Phytotaxa. 2014;183: 239–253.
- 21. Cabral TS, Clement CL, Baseia IG. Amazonian phalloids: new records for Brazil and South America. Mycotaxon. 2015;130: 315–320.
- 22.
Kirk PM, Cannon PF, Minter DW, Stalpers JA. Ainsworth and Bisby's Dictionary of the Fungi. 10th Edition. UK: CABI Publishing, Oxford; 2008.
- 23. Guzmán G, Cortés-Pérez A, Guzmán-Dávalos L, Ramírez-Guillén F, Sánchez-Jácome MR. An emendation of Scleroderma, new records, and review of the known species in Mexico. Rev Mexicana Biodiv. 2013;S173–S191.
- 24. Phosri C, Martín MP, Watling R, Jeppson M, Sihanonth P. Molecular phylogeny and re-assessment of some Scleroderma spp. (Gasteromycetes). An Jar Bot Madrid. 2009:66S1: 83–91.
- 25. Rusevska K, Karadelev M, Phosri C, Dueñas M, Watling R, Martín MP. Rechecking the genus Scleroderma (Gasteromycetes) from Macedonia using barcoding approach. Turk J Bot. 2014;38: 375–385.
- 26. Kumla J, Suwannarach N, Bussaban B, Lumyong S. Scleroderma suthepense, a new ectomycorrhizal fungus from Thailand. Mycotaxon. 2013;123: 1–7.
- 27. Hennings P. Fungi amazonici a. cl. Ernesto Ule collecti: 1. Hedwigia. 1904;43: 154–186.
- 28. Viégas AP. Alguns fungos do Brasil IX: Agaricales. Bragantia. 1945;5(9): 583–595.
- 29. Rick J. Basidiomycetes Eubasidii no Rio Grande do Sul. Brasília. Iheringia. 1961:9: 451–480.
- 30. Guzmán G. Monografía del género Scleroderma Pers. emend. Fr. (Fungi, Basidiomycetes). Darwiniana. 1970;16: 233–407.
- 31. Bononi VLR, Trufem SFB, Grandi RAP. Fungos macroscópicos do Parque Estadual das Fontes do Ipiranga depositados no Herbário do instituto de Botânica. Rickia. 1981;9: 37–53.
- 32. Baseia IG, Milanez AI. First record of Scleroderma polyrhizum Pers. (Gasteromycetes) from Brazil. Acta Bot Brasilica. 2000;14(2): 181–184.
- 33. Giachini AJ, Oliveira VL, Castellano MA, Trappe JM. Ectomycorrhizal Fungi in Eucalyptus and Pinus Plantations in Southern Brazil. Mycologia. 2000:92(6): 1166.
- 34. Sobestiansky G. Contribution to a Macromycete survey of the states of Rio Grande do Sul and Santa Catarina in Brazil. Braz Arch Biol Technol. 2005;48: 437–457.
- 35. de Meijer AAR Preliminary list of the macromycetes from the Brazilian State of Paraná. Bol Mus Bot Munich. 2006;68: 1–55.
- 36. Cortez VG, Baseia IG, Silveira RMB. Gasteroid mycobiota of Rio Grande do Sul, Brazil: Boletales. J Yeast Fungal Res. 2011;2: 44–52. Available online http://www.academicjournals.org/JYFR.
- 37. Drechsler-Santos ER, Wartchow F, Baseia IG, Gibertoni TB, Cavalcanti MAQ. Revision of the Herbarium URM I. Agaricomycetes from the semi-arid region of Brazil. Mycotaxon. 2008;104: 9–18.
- 38. Gurgel FE, Silva BDB, Baseia IG. New records of Scleroderma from Northeastern Brazil. Mycotaxon. 2008;105: 399–405.
- 39. Crous PW, Wingfield MJ, Richardson DM, Leroux JJ, Strasberg D, Edwards J, et al. Fungal Planet description sheets: 400–468. Persoonia. 2016;36: 316–458. pmid:27616795
- 40.
Grgurinovic CA. Larger fungi of South Australia. Adelaide: The Botanic Gardens of Adelaide;1997.
- 41. Calonge FD. Gasteromycetes. I. Lycoperdales, Nidulariales, Phallales, Sclerodermatales, Tulostomatales. Flora Mycologica Iberica. 1998;3: 1–271.
- 42. Guzmán G, Ovrebo CL. New observations on sclerodermataceous fungi. Mycologia. 2000;92: 171–179.
- 43. Guzmán G, Ramírez-Guillén F, Miller OK Jr., Lodge DJ, Timothy JB. Scleroderma stellatum versus Scleroderma bermudense: the status of Scleroderma echinatum and the first record of Veligaster nitidum from the Virgin Islands. Mycologia. 2004;96: 1370–1379. pmid:21148960
- 44.
Kornerup A, Wanscher JH. Methuen handbook of colour. 3rd ed. Eyre Methuen. London; 1978.
- 45. Gardes M, Bruns TD. ITS primers with enhanced specificity for Basidiomycetes-applications to the identification of mycorrhizae and rusts. Mol Ecol. 1993;1: 113−118.
- 46.
White TJ, Bruns T, Taylor J. Amplification and direct sequencing of fungal ribosomal rNa genes for phylogenetics. In: Innes MA, Gelfand DH, Sninsky JJ, White TJ PCR protocols. A guide to methods and applications. Academic Press, Inc., San Diego, California; 1990. pp. 315−322.
- 47. Martín MP, Winka K. Alternative methods of extracting and amplifying DNA from lichens. Lichenologist. 2000;32: 189−196.
- 48. Cochrane G, Karsch-Mizrachi I, Nakamura Y. The inter- national nucleotide sequence database collaboration. Nucl Acids Res. 2011;39: D15–18. pmid:21106499
- 49. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389−3402. pmid:9254694
- 50.
Swofford DL. PAUP* Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer associates, Sunderland, Massachusetts; 2003.
- 51. Huelsenbeck JP, Ronquist F. Mr. Bayes: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17: 754–755. pmid:11524383
- 52. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22: 2688–2690. pmid:16928733
- 53.
Miller MA, Holder MT, Vos R, Midford PE, Liebowitz T, Chan L,Hoover P, et al. The CIPRES Portals. CIPRES. 2009; URL:http://www.phylo.org/sub_sections/portal. Accessed: 2016–04–18.
- 54. Binder M, Bresinsky A. Derivation of a polymorphic lineage of Gasteromycetes from boletoid ancestors. Mycologia. 2002;94(1): 85–98. pmid:21156480
- 55. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39: 783–791.
- 56. Huelsenbeck JP, Larget, B, Swofford DL. A compound Poisson process for relaxing the molecular clock. Genetics. 2000;154: 1879–1892. pmid:10747076
- 57. Larget B, Simon D. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol. 1999;16: 750–759.
- 58. Rodríguez F, Oliver JF, Martín A, Medina JR. The general stochastic model of nucleotide substitution. J Theor Biol. 1990;142: 485–501. pmid:2338834
- 59. Page RDM. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996;12: 357–358. pmid:8902363
- 60. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 2004;91: 1446–1480. pmid:21652303
- 61. Wilson AW, Binder M, Hibbett D. Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota). New Phytol. 2012;194: 1079–1095. pmid:22471405
- 62. Watling R, Sims KP. Taxonomic and floristic notes on some larger Malaysian fungi IV (Scleroderma). Fungi in forest ecosystems; systematics, diversity and ecology. Mem New York Bot Gard. 2004;89: 93–6.
- 63. Silva JMC, Rylands AB, Fonseca GAB. The fate of the Amazonian areas of endemism. Conserv Biol. 2005;19(3): 689–694.
- 64. Haffer J Hypotheses to explain the origin of species in Amazonia. Braz J Biol. 2008;68(4): 917–947.
- 65.
Luizão FJ, Vasconcelos HL. Floresta Tropical Úmida (Manaus). Site 1.Os Sites e o Programa Brasileiro de Pesquisas Ecológicas de Longa Duração. Ed. Belo Horizonte, UFMG, Belo Horizonte, Brasil; 2002.
- 66. Fearnside PM. The roles and movements of actors in the deforestation of Brazilian Amazonia. Ecol Soc. 2008;13: 23. http://www.ecologyandsociety.org/vol13/iss1/art23/
- 67. Clement CR, Santos RP, Desmouliere SJM, Ferreira EJL, Neto JTF. Ecological Adaptation of Wild Peach Palm, Its In Situ Conservation and Deforestation-Mediated Extinction in Southern Brazilian Amazonia. PLoS ONE. 2009;4(2): e4564. pmid:19238213
- 68. Benchimol M, Peres CA. Widespread Forest Vertebrate Extinctions Induced by a Mega Hydroelectric Dam in Lowland Amazonia. PLoS ONE. 2015;10(7): e0129818. pmid:26132139
- 69. Brook BW, Bradshaw CJA, Koh LP, Sodhi NS. Momentum Drives the Crash: Mass Extinction in the Tropics. Biotropica. 2006;38: 302–305.
- 70. Roy M, Schimann H, Braga-Neto R, Da Silva RAE, Duque J, Frame D, et al. Diversity and distribution of cctomycorrhizal fungi from Amazonian lowland white-sand forests in Brazil and French Guiana. Biotropica. 2016;48(1): 90–100.
- 71. Cracraft J. Historical biogeography patterns of differentiation within the South American avifauna: areas of endemism. Ornithol Monogr. 1985; 36: 49–84.
- 72. Terborgh J, Robinson SK, Parker TA III, Munn CA, Pierpoint N. Structure and organization of an Amazonian Forest bird community. Ecol Monogr. 1990; 60(2): 213–238.
- 73. Thiollay JM. Structure, density and rarity in an Amazonian rainforest bird community. J Trop Ecol. 1994;10(4): 449–481.
- 74. Hopkins MJG. Modelling the known and unknown plant biodiversity of the Amazon Basin. J Biogeogr. 2007;34: 1400–1411.
- 75. Viera ICG, Toledo PM, Silva JMC, Higuchi H. Deforestation and threats to the biodiversity of Amazonia. Braz. J. Biol. 2008; 68:949–956. http://www.scielo.br/pdf/bjb/v68n4s0/a04v684s.pdf pmid:19197467
- 76. Milliken W, Zappi D, Sasaki D, Hopkins M, Pennington RT. Amazon vegetation: how much don’t we know and how much does it matter? Kew Bull. 2011;65: 1–19.
- 77. Malhado ACM, Ladle RJ, Whittaker RJ, Neto, JAO, Malhi Y, ter Steege H. The ecological biogeography of Amazonia. Front Biogeogr. 2013;5: 103–112. http://www.escholarship.org/uc/item/9qw3j2v2.
- 78. Gibbons JW, Scott DE, Ryan TJ, Buhlmann KA, Tuberville TD, Metts B, et al. The global decline of reptiles, deja’ vu amphibians. BioScience. 2000;50: 653–666. digitalcommons.butler.edu/facsch_papers/536/.
- 79. Hayes TB, Falso P, Gallipeau S, Stice M. The cause of global amphibian declines: a developmental endocrinologist’s perspective. J Exp Biol 2010;213: 921 933. pmid:20190117
- 80. Cameron SA, Lozier JD, Strange JP, Koch JB, Cordes N, Solter LF, et al. Patterns of widespread decline in North American bumble bees. Proc Natl Acad Sci U S A. 2011;108(2): 662–667. pmid:21199943
- 81. Gargas A, Trest MT, Christensen M, Volk TJ, Blehert DS. Geomyces destructans sp. nov. associated with bat white-nose syndrome. Mycotaxon. 2009;108: 147–154. http://botit.botany.wisc.edu/toms_fungi/147gargas9-73.pdf.
- 82. Frick WF, Pollock JF, Hicks AC, Langwig KE, Reynolds DS, Turner GG, et al. An emerging disease causes regional population collapse of a common North American bat species. Science. 2010;329: 679–682. pmid:20689016
- 83. Lorch JM, Meteyer CU, Behr MJ, Boyles JG, Cryan PM, Hicks AC, et al. Experimental infection of bats with Geomyces destructans causes white-nose syndrome. Nature. 2011;480: 376–378. pmid:22031324
- 84. Casadevall A. Fungal virulence, vertebrate endothermy, and dinosaur extinction: is there a connection? Fungal Genet Biol. 2005;42: 98–106. pmid:15670708
- 85. Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, et al. Emerging fungal threats to animal, plant and ecosystem health. Nature. 2012;484: 186–184. pmid:22498624
- 86. Veresoglou SD, Halley JM, Rillig MC. Extinction risk of soil biota. Nat Commun. 2015; 6: 8862. pmid:26593272
- 87. Tibbett M, Sanders FE. Ectomycorrhizal symbiosis can enhance plant nutrition through improved access to discrete organic nutrient patches of high resource quality. Ann Bot 2002;89(6): 783–789. pmid:12102534
- 88. Mittermeier RA, Myers N, Thomsen JB, Da Fonseca GAB, Olivieri S. Biodiversity Hotspots and Major Tropical Wilderness Areas: Approaches to Setting Conservation Priorities. Conserv Biol. 1998;12: 516–520.