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| Diversity indexes and richness metrics of culturable fungal communities within the three habitats in the Heshang Cave, central China.
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Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent metho...
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... the coverage of fungal community was over 0.87 which indicated the data can reflect the culturable fungal community in weathered rocks. The coverage increased from 0.87 to 0.89 with the increase of cutoff from 1 to 5% (Table 2). Meanwhile the α diversity decreased with the increase of cutoff. ...
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... the α diversity decreased with the increase of cutoff. Chao and Shannon indexes decreased from 26 to 20, 1.91 to 1.84, respectively ( Table 2). The PD index was 0.86, 0.80, and 0.86, respectively with a cutoff of 1, 3, and 5% ( Table 3). ...
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... coverage of fungal community retrieved from sediments increased from 0.61 to 0.74 with the increase of cutoff from 1 to 5% (Table 2). Meanwhile the α diversity decreased with the increase of cutoff. ...
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... the α diversity decreased with the increase of cutoff. Chao and Shannon indexes decreased from 104 to 63, 3.41 to 2.86, respectively ( Table 2). The PD index was 4.00, 3.72, and 3.85, respectively with a cutoff of 1, 3, and 5% ( Table 3). ...
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... coverage of fungal community was between 0.92 and 0.94 with different cutoff ( Table 2). Shannon indexes decreased from 2.03 to 1.59 with the increase of cutoff from 1 to 5% whereas Chao showed a maximum of 21 with the cutoff of 3% ( Table 2). ...
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... coverage of fungal community was between 0.92 and 0.94 with different cutoff ( Table 2). Shannon indexes decreased from 2.03 to 1.59 with the increase of cutoff from 1 to 5% whereas Chao showed a maximum of 21 with the cutoff of 3% ( Table 2). The PD index ( Table 3) showed a minimum of 0.77 at the cutoff of 3% ( Table 3). ...
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... OTU richness decreased with the increase of cutoff from 1 to 5% in three habitats as indicated by Chao estimator ( Table 2). The number of OTUs decreased from 14 to 9, 11 to 10, and 46 to 34 in bat guanos, weathered rocks and sediments with the increase of cut off values respectively. ...
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... number of OTUs decreased from 14 to 9, 11 to 10, and 46 to 34 in bat guanos, weathered rocks and sediments with the increase of cut off values respectively. The α-diversity of fungal community was relatively low in bat guanos and high in sediments as indicated by Shannon and Simpson indexes ( Table 2). The β-diversity of fungal communities showed significant differences both in fungal composition and their abundance between each two habitats with weighted-UniFrac method despite of the different cutoff of OTUs (P < 0.01, Table 4). ...
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... genus level, 33 genera were observed and only five of them were shared by two habitats; others were exclusively present in one specific habitat. Fungal diversity was the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes ( Table 2). These results were consistent with the results of fungal communities in caves around the world ( Vaughan et al., 2008;Vanderwolf et al., 2013). ...
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... Aspergillus was the most frequent (63 %) and had the highest number of taxa on all substrates, followed by Penicillium (32 %) and Talaromyces (3 %). Our results are similar to those of previous studies that have also reported Aspergillus, Penicillium, and Talaromyces as the most abundant fungi in cave environments worldwide (Nováková 2009, Vanderwolf et al. 2013, Man et al. 2015, Zhang et al. 2017, Chlebicki & Jakus 2019, Cunha et al. 2020, Zhang et al. 2020, Sanchez-Moral et al. 2021, Visagie et al. 2021, Alves et al. 2022. ...
... In contrast to other studies that showed Penicillium as the most common in guano and soil/sediment from caves (Novaková 2009, Man et al. 2015, Zhang et al. 2020, Wasti et al. 2021, our results highlighted Aspergillus as the most abundant genus. For example, in a cave complex located in an arid region in Azerbaijan, Aspergillus was the most common in sediment (Mazina et al. 2023). ...
The study of the Brazilian cave mycobiota has revealed a rich but highly diverse assemblage of fungi, with Aspergillus, Penicillium, and Talaromyces being the most frequently reported genera. The present study investigated the airborne fungi and fungi obtained from the bodies of bats, guano, and the soil/sediment from the caves Urubu (in the Atlantic Forest) and Furna Feia (in the Caatinga dryland forest) in the Northeast region of Brazil. Fungal strains were identified based on morphological features and multilocus phylogenetic analyses of ITS, beta-tubulin (BenA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) sequences. A total of 86 isolates were obtained, representing Aspergillus (34), Penicillium (20), Talaromyces (2), and 30 isolates belonging to other genera that will be reported on elsewhere. These isolates were identified as 18 Aspergillus, nine Penicillium, and one Talaromyces species. Eight of the species identified are reported for the first time from a cave environment. Four species showed unique morphological features and phylogenetic relationships, and are newly described. These include two new species of Aspergillus (A. alvaroi sp. nov. and A. guanovespertilionum sp. nov.), one of Penicillium (P. cecavii sp. nov.), and one of Talaromyces (T. potiguarorum sp. nov.). Our study increases the awareness and known richness of the Brazilian and global fungal diversity found in caves.
... For the PCR reactions, a total volume of 50 µL contained 25 µL of Premix Taq (Takara Biotechnology, Dalian Co., Ltd., Dalian, China), 1 µL each of the tag-encoded primers (10 mM), 3 µL of DNA template (20 ng/µL) and 20 µL of RNAasefree water. PCR amplifications were performed in triplicate under conditions described previously [7]. The PCR products were qualified by a Nanodrop 2000 spectrophotometer ...
... In subterranean karst caves, substrates such as air, sediments, weathered rocks, guano, dripping water, bat skin/fur, bat bones, dung, wood, earthworm casts and insects have been commonly sampled for taxonomic and mycobiome studies [4,6,7,14,16]. In our survey, we found that the sediments had higher values of Chao 1 metrics, ACE index, Shannon index, observed-species an PD metric than the weathered rock samples. ...
... Ascomycota dominated all samples, followed by Basidiomycota (Figure 2). This result aligns with those of cave mycology studies based on culture and non-culture methods [4,7,16,37,38]. Among the fungal taxa reported from caves and mines worldwide before 2013, Ascomycota (69.1%) and Basidiomycota (20%) were the dominant groups [6]. ...
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems.
... Nearest neighbor interchange (NNI) of quick searches was selected for ML heuristic analysis. The bootstrap analysis was run for 1000 replicates (Man et al., 2015). The 16S rRNA sequencing data of 25-M has been submitted to GenBank with accession number OR512352. ...
... In the case of a study focused on description of the diversity of easily cultivable endophytic fungi, a single culture medium such as PDA (Ibrahim et al. 2021) can be used. To increase the number of retrieved taxa, two or more different culture media can be employed in addition to PDA (Man et al. 2015;Gong et al. 2019). Supplementation of culture medium with plant material from the host species can also be used to improve the recovery of endophytic fungi (Mourad et al. 2018). ...
Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.
... Handful of studies report the microfungi of cave environment. Man et al. (2015) have reported for the f irst-time the presence of fungal communities its functions in cave ecosystems in a natural pristine cave of central China. Recent work on diversity of fungal species in Mandeepkhol cave, Chhattisgarh report 54 species belonging to 16 genera and two mycelia sterilia (Karkun et al. 2012). ...
... (Nguyen et al.2015) was used to reconstruct the phylogenetic tree. (Man et al. 2015).In India, Karkun et al. (2012) worked on the diversity of fungal species in Mandeepkhol cave, Chhattisgarh and reported 54 species belonging to 16 genera and two mycelia sterilia. ...
First report on occurance of clonostachys in cake ecosystem from India
... Usually, bacterial communities living on outcrop carbonate rocks exposed to sunlight and rainfall were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria, whereas fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes, and Leotiomycetes (Choe et al., 2018). Microbial communities inhabiting the surfaces of carbonate rocks in permanently dark caves (Man et al., 2015;Yun et al., 2016;Zhu et al., 2021) are far less studied than those associated with outcrop rocks. Rock surfaces in subsurface caves are directly exposed to air, aerosol, and water vapor (high humidity), as well as a variety of physicochemical and biological dissolutionprecipitation and oxidation-reduction reactions, leading with time to weathering and the formation of various secondary minerals (Aloisi et al., 2006;Gallagher et al., 2012). ...
... Highly diverse bacterial communities were detected from the weathered rocks in caves with the dominance of Proteobacteria, Actinomycetes, and Firmicutes (Yun et al., 2016;Zhu et al., 2019Zhu et al., , 2021Ma et al., 2021). In contrast, the diversity of fungi is relatively low due to the limited input of organic matter by photosynthesis in caves (Lee et al., 2012;Man et al., 2015). It was estimated that the content of organic matter in caves is three orders of magnitude less than that on the surface (Lavoie et al., 2010). ...
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.
... The organisms have to adapt to a large panel of factors that are not constant-temperature, carbon sources, pollutants, etc. [9,10]. The cave environment is unique for its lack of light and constant climate, and where the contaminations with pollutants can be minimal in its deepest parts [11][12][13][14]. As opposed to the relatively pristine cave environment, hospital environments are highly contaminated with and antibiotics. ...
The opportunistic infections with Gram-negative bacilli are frequently reported. The clinical studies are focused on the course of human infectious and very often the source of infection remain unclear. We aim to see if the Gram-negative bacilli isolated from a non-contaminated environment—the caves—are reported in human infections. Eleven samples were collected from six Romanian caves. We used the standard procedure used in our clinical laboratory for bacterial identification and for antibiotic susceptibility testing of the cave isolates. Out of the 14 bacterial strains, three isolates are Gram-negative bacilli—one isolate belong to Hafnia alvei and two strains belong to Sphingomonas paucimobilis. We screened for the published studies—full-text original articles or review articles—that reported human infections with S. paucimobilis and H. alvei. Data sources—PubMed and Cochrane library. We retrieved 447 cases from 49 references—262 cases (58.61%) are S. paucimobilis infections and 185 cases (41.39%) are H. alvei infections. The types of infections are diverse but there are some infections more frequent; there are 116 cases (44.27%) and many infections of the bloodstream with S. paucimobilius (116 cases) and 121 cases (65.41%) are urinary tract infections with H. alvei. The acquired source of the bloodstream infections is reported for 93 of S. paucimobilis bloodstream infections—50 cases (43%) are hospital-acquired, and 40 cases (37%) are community-acquired. Most of the infections are reported in patients with different underlying conditions. There are 80 cases (17.9%) are reported of previously healthy persons. Out of the 72 cases of pediatric infections, 62 cases (86.11%) are caused by S. paucimobilis. There are ten death casualties—three are H. alvei infections, and seven are S. paucimobilis infections.
... This dolomite, bats excrement, dead vertebrates and invertebrates provide organic matter that supports the growth of various microorganisms. The decomposition of this organic matter is typically carried out by fungi and bacteria (Man et al. 2015, Pusz et al. 2015. ...
... The Gcwihaba Cave was found to be species-rich with most species isolated in low numbers, except for A. sydowii (43 strains) and A. subalbidus (13 strains) that dominated communities. Fungal surveys from caves often find Aspergillus and Penicillium to be very common (Johnson et al. 2013, Man et al. 2015, , Zhang et al. 2017, Zhang et al. 2020, Sanchez-Moral et al. 2021. Unfortunately, most of these surveys identified strains based on the ITS barcode which is not reliable on a species level in both of these genera (Houbraken et al. 2020). ...
A fungal survey of the Gcwihaba Cave from Botswana found Aspergillus to be one of the more common fungal genera isolated. The 81 Aspergillus strains were identified using CaM sequences and comparing these to a curated reference dataset. Nineteen species were identified representing eight sections (sections Candidi , Circumdati , Flavi , Flavipedes , Nidulantes , Nigri , Terrei and Usti ). One strain could not be identified. Morphological characterisation and multigene phylogenetic analyses confirmed it as a new species in section Flavipedes and we introduce it below as A. okavangoensis . The new species is most similar to A. iizukae , both producing conidiophores with vesicles typically wider than 20 µm. The new species, however, does not produce Hülle cells and its colonies grow slower than those of A. iizukae on CYA at 37 °C (14–15 vs 18–21 mm) and CREA (15–16 vs 23–41mm).
... Cave microbiota are metabolically versatile and are involved in important lithogenic processes such as speleothem deposition, but also in unwanted changes such as color covering spots and litholitic processes such as bioweathering of rocks and minerals [16][17][18][19]. Any biological activity that affects the appearance and integrity of the materials is known as "biodeterioration" [20,21]. ...
... Table S2). Ascomycota is usually the dominating phylum along the cave mycobiota, with Zygomycota and Basidiomycota being less present [4,[13][14][15]18,[66][67][68][69]. Penicillium (9 isolates) was the most apparent genus followed by Clonostachys (5), Fusarium (4), Doratomyces (4), Cephalotrichum (3), Talaromyces (2), Acremonium (2), Xenoacremonium (2), Trichurus (1) and Cladosporium (1). ...
... Penicillium (9 isolates) was the most apparent genus followed by Clonostachys (5), Fusarium (4), Doratomyces (4), Cephalotrichum (3), Talaromyces (2), Acremonium (2), Xenoacremonium (2), Trichurus (1) and Cladosporium (1). Penicillium [4,15,18,21,29,[66][67][68][69][70][71][72][73][74] and Fusarium [4,18,21,29,74,66,72] are two of the most reported fungi present in caves. Clonostachys [21,29,68,72,74], Doratomyces [21,[66][67][68]71,72], Cephalotrichum [21,29,68,69,74], Talaromyces [21,68,69,[72][73][74], Acremonium [15,18,21,29,[66][67][68][69]72,75,76], Xenoacremonium [68], Trichurus [70,71] and Cladosporium [4,15,18,21,29,[66][67][68][69][70]72,74,75], were also identified in previous studies. ...
The present study concerns the serious issue of biodeterioration of the caves belonging to natural and cultural heritage sites due to the development of various microorganisms. Thus, a series of 18 essential oils (EOs) extracted from various Greek plants were evaluated in vitro (concentrations of 0.1, 0.2, 0.5, 1.0 and 5.0% v/v) against 35 bacterial and 31 fungi isolates (isolated from a Greek cave) and the antimicrobial activity was evident through the changes in optical density of microbial suspensions. In continuance, eight (8) representative bacterial and fungal isolates were further used to evaluate the minimum inhibitory concentration (MIC) and non-inhibitory concentration (NIC) values of the most effective EOs. According to the results, two EOs of Origanum vulgare were the most effective by inhibiting the growth of all the tested microorganisms at 0.1% (v/v), followed by that of Satureja thymbra which inhibited all bacterial isolates at 0.1% (v/v) and fungal isolates at 0.1, 0.2 and 0.5% (v/v) (depending on the isolate). The MIC ranged between 0.015-0.157 and 0.013-0.156 (v/v) for the bacterial and fungal isolates respectively, depending on the case. The current study demonstrated that conventional biocides may be replaced by herbal biocides with significant prospects for commercial exploitation.
... These estimates are surprisingly high and contrast those for soil micro-organisms in general (~1% of microorganisms e Davis et al., 2005) and fungi specifically. Although many studies have combined both direct environmental sequencing and pure-culturing approaches (e.g., Pitk€ aranta et al., 2008;Daghino et al., 2012;Man et al., 2015), consistent and comparable approaches e such as simultaneous MiSeq analyses of ITS2 amplicons described here e have been lacking. ...
Current environmental change predictions forecast intensified drought conditions. It is becoming increasingly evident that plant communities are sensitive to drought and that soil-inhabiting microbial communities vary along precipitation gradients. However, the drought sensitivity of microbial communities in general and that of soil fungi in particular remains unclear, even though understanding their responses to adverse environmental conditions is vital for better understanding of ecosystem service provisioning. We sampled soils at two sites with established experiments that imposed extreme, chronic drought to assess fungal community responses. We analyzed fungal communities using both culture-dependent and -independent tools and MiSeq-sequenced communities from colony forming units (CFU-PCR) on a drought simulating medium and from environmental DNA (ePCR), to compare the conclusions derived from these two methods. Our data from the two approaches consistently indicate that the composition of fungal communities is not affected by the drought treatment, whereas – based on the CFU-PCR but not ePCR data – their richness and diversity increased under drought conditions at the more mesic of the two sites. Further, based on the direct comparisons of CFU-PCR and ePCR, we estimate that more than 10% of the fungal community and more than 20% of the ascomycetes were culturable. We conclude that although recent research indicates that plant and bacterial communities respond to drought, fungal community responses are more variable, particularly in experiments that impose chronic drought under field conditions.
