Abstract
Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumina HiSeq sequencing of fungal rRNA-ITS1 gene across different habitats. In total 793,502 ITS1 reads and 2,179 OTUs from 778 Mb reads after stringent quality control (Q30) and 453 genera, 72 orders and 19 classes within 6 phyla were detected. Ascomycota (42% OTUs) dominated across the five habitats. Shannon-Wiener index varied from 1.25 to 7.62 and community richness was highest in drip waters, followed by weathered rocks, bat guanos, sediments, and air samples. Mycobiomes displayed specificity to five habitats and more distinct OTUs were found in weathered rocks (12%) and drip waters (9%). In contrast, only 6.60% core OTUs were shared by five habitats. Notably, weathered rocks possessed more indicator groups and were revealed for the first time to be dominated by Sordariomycetes (43%). The community richness of air mycobiomes increased from cave entrance to the innermost part and dominated by the indicator groups of Penicillium mallochii (>30%) and P. herquei (>9%). Our work represents the largest attempt to date to a systematical investigation of oligotrophic solution-cave-associated mycobiomes in China. Our discovery of high diversity of mycobiomes in Heshang Cave also suggests that eukaryotic microorganisms may play a crucial role in subsurface environments.
Highlights
As the second largest kingdom of eukaryotic life, fungi are more diverse and widely distributed in aquatic and terrestrial ecosystems, such as soils (Ritz and Young, 2004), lakes and deep-sea (Shearer et al, 2007; Nagahama and Nagano, 2012), caves and rock surfaces (Sterflinger, 2000; Gorbushina, 2007; Vanderwolf et al, 2013)
Drip waters have the lowest concentrations of Ca2+, Mg2+, Cl−, NO3−, and SO42− compared with other samples (Supplementary Table 2)
Diverse mycobiomes were revealed by high-throughput sequencing methods with 453 genera, 72 orders and 19 classes within 6 phyla in five habitats of Heshang Cave
Summary
As the second largest kingdom of eukaryotic life, fungi are more diverse and widely distributed in aquatic and terrestrial ecosystems, such as soils (Ritz and Young, 2004), lakes and deep-sea (Shearer et al, 2007; Nagahama and Nagano, 2012), caves and rock surfaces (Sterflinger, 2000; Gorbushina, 2007; Vanderwolf et al, 2013). Even if great efforts have been put on uncovering the diversity of mycobiomes in different niches via generation sequencing (NGS) technologies (Lentendu et al, 2011; Shi et al, 2014; Duarte et al, 2015; Abdelfattah et al, 2016), it still lags behind in comparison with those of the prokaryotic microbiomes. Increasing investigations via NGS techniques in recent years successfully revealed the diversity of the prokaryotic microbiomes (Zhang et al, 2012; Blasiak et al, 2014; Walsh et al, 2016; Yun et al, 2016a) and provided enormous amount of data on the premise of low price (Caporaso et al, 2012; Degnan and Ochman, 2012), while few NGS studies focused on systematic investigations of the diversity of mycobiomes in pristine karst caves (Vaughan et al, 2015). Fungi have long been recorded in caves 225 years ago (Dobat, 1967), they have received far less attention and limited our deeper understanding for the diversity and potential roles of fungi in subterranean ecosystems
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