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Phylogenetic diversity of culturable fungi in the Heshang Cave, central China.

Man B, Wang H, Xiang X, Wang R, Yun Y, Gong L - Front Microbiol (2015)

Bottom Line: At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively.Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly.Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China.

ABSTRACT
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 method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems.

No MeSH data available.


Phylogenetic dendrogram of culturable fungal rRNA-ITS gene sequences from representative OTUs with 5% cutoff in the Heshang Cave, central China. Maximum Likelihood algorithm with Kimura’s two parameter-Gamma distributed model; 1,000 bootstrap replicates were performed and values with >50% are shown in the tree. Sequences obtained in the present study and their GenBank accession numbers are in bold. Numbers in parenthesis indicate the sequence numbers from bat guanos (blue), weathered rocks (red), and sediments (green), respectively. U stands for unclassified.
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Figure 2: Phylogenetic dendrogram of culturable fungal rRNA-ITS gene sequences from representative OTUs with 5% cutoff in the Heshang Cave, central China. Maximum Likelihood algorithm with Kimura’s two parameter-Gamma distributed model; 1,000 bootstrap replicates were performed and values with >50% are shown in the tree. Sequences obtained in the present study and their GenBank accession numbers are in bold. Numbers in parenthesis indicate the sequence numbers from bat guanos (blue), weathered rocks (red), and sediments (green), respectively. U stands for unclassified.

Mentions: All isolates obtained from 42 samples at 14 sampling sites were sequenced. Most sequences showed high affiliations (identity ≥ 98%) with their best matches in the NCBI database. The ITS sequences were clustered into 41 OTUs with a cutoff of 5%, which fell into 33 genera within 15 orders of three phyla (Figure 2). Ascomycota clearly dominated the recovered fungal community with 33 OTUs (80% of the total OTUs). In contrast, only five OTUs belonged to Basidiomycota and three to Zygomycota (Figure 2). At the taxonomic level of order, the culturable fungal community had nine orders and two unclassified members in Ascomycota, three in Basidiomycota and two in Zygomycota (Figure 2). Hypocreales (11 OTUs) and Eurotiales (10 OTUs) were the most abundant two orders (Figure 2). At genus level, the most frequently observed OTUs showed high affinities to Penicillium (Figure 2).


Phylogenetic diversity of culturable fungi in the Heshang Cave, central China.

Man B, Wang H, Xiang X, Wang R, Yun Y, Gong L - Front Microbiol (2015)

Phylogenetic dendrogram of culturable fungal rRNA-ITS gene sequences from representative OTUs with 5% cutoff in the Heshang Cave, central China. Maximum Likelihood algorithm with Kimura’s two parameter-Gamma distributed model; 1,000 bootstrap replicates were performed and values with >50% are shown in the tree. Sequences obtained in the present study and their GenBank accession numbers are in bold. Numbers in parenthesis indicate the sequence numbers from bat guanos (blue), weathered rocks (red), and sediments (green), respectively. U stands for unclassified.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4612708&req=5

Figure 2: Phylogenetic dendrogram of culturable fungal rRNA-ITS gene sequences from representative OTUs with 5% cutoff in the Heshang Cave, central China. Maximum Likelihood algorithm with Kimura’s two parameter-Gamma distributed model; 1,000 bootstrap replicates were performed and values with >50% are shown in the tree. Sequences obtained in the present study and their GenBank accession numbers are in bold. Numbers in parenthesis indicate the sequence numbers from bat guanos (blue), weathered rocks (red), and sediments (green), respectively. U stands for unclassified.
Mentions: All isolates obtained from 42 samples at 14 sampling sites were sequenced. Most sequences showed high affiliations (identity ≥ 98%) with their best matches in the NCBI database. The ITS sequences were clustered into 41 OTUs with a cutoff of 5%, which fell into 33 genera within 15 orders of three phyla (Figure 2). Ascomycota clearly dominated the recovered fungal community with 33 OTUs (80% of the total OTUs). In contrast, only five OTUs belonged to Basidiomycota and three to Zygomycota (Figure 2). At the taxonomic level of order, the culturable fungal community had nine orders and two unclassified members in Ascomycota, three in Basidiomycota and two in Zygomycota (Figure 2). Hypocreales (11 OTUs) and Eurotiales (10 OTUs) were the most abundant two orders (Figure 2). At genus level, the most frequently observed OTUs showed high affinities to Penicillium (Figure 2).

Bottom Line: At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively.Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly.Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China.

ABSTRACT
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 method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems.

No MeSH data available.