Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data

Pfendler, Stéphane; Karimi, Battle; Maron, Pierre‐Alain; Ciadamidaro, Lisa; Valot, Benoı̂t; Bousta, Faisl; Alaoui-Sossé, Laurence; Alaoui-Sossé, Badr; Aleya, Lotfi

doi:10.1016/j.scitotenv.2017.10.054

Cited by 53 publications

(54 citation statements)

References 57 publications

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“…The potential reason is that the fungal assemblages in air may frequently communicate between the inside and outside environment, while those in rock and sediment are much more stable and adapted to the local environment, where temperature has been shown to be one of the key factors influencing fungal growth, reproduction and distribution (Dang, Schindler, Chauvet, & Gessner, ; Rajashekhar & Kaveriappa, ; Suberkropp, ) by regulating metabolic rates (Sokolova & Lannig, ). Consistent with our results, Pfendler et al () also found that microbial communities in different caves were significantly different, probably due to the different microenvironmental and physiochemical properties (Adetutu et al, ; Pfendler et al, ). Due to the combined effects of climate, niche conservatism, and rates of evolutionary radiation and extinction, the richness of nearly all terrestrial and marine microorganisms and soil fungi is known to be negatively related to the increasing latitude (Mittelbach et al, ; Tedersoo et al, ).…”

Section: Discussionsupporting

confidence: 91%

“…Cloutier et al () reported a high relative abundance of Zygomycota (up to 49.8% in some sites) with endogenous carbon in caves. Similarly, in the study of Pfendler et al (), Mortierella was highly dominant in four show caves. Therefore, the culture‐based method, which obtained a high relative abundance of Zygomycota in previous studies, may not be as biased as reported (Vanderwolf et al, ).…”

Section: Discussionsupporting

confidence: 66%

“…However, a study by Cloutier, Carmichael, Carson, Madritch, and Bräuer () revealed that exogenous carbon changed the fungal community composition but had no influence on diversity. Pfendler et al () investigated the biofilm biodiversity on rocks in five caves frequently visited by tourists in France and Switzerland and found that fungi in biofilms in caves are less diverse than bacteria and that the fungal communities were different among the caves.…”

Section: Introductionmentioning

confidence: 99%

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Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

Zhang

Cai

2019

Journal of Biogeography

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Aim Previous studies primarily based on the culture method have revealed that caves host a high fungal diversity and that exogenous carbon sources influence fungal communities. Here, we assess the fungal diversity and distribution patterns in karst caves in Southwest China and reveal the major factors that shape the fungal communities. Location Southwest China. Methods Samples of air, rock, sediment and water were collected from eight caves in Southwest China. Using high‐throughput sequencing of the internal transcribed spacer 1 region of fungal rDNA, we examined the cave fungal communities in Southwest China and studied their correlations with potentially influential factors, such as substrate, cave, location and environmental variables. Results Approximately 10,000 fungal operational taxonomic units (OTUs) spanning 15 phyla were obtained. The highest diversity genus was Penicillium, while Mortierella had the highest relative abundance. Compared with air and rock samples, sediment and water samples harboured higher diversity and distinct communities. Substrate and cave were revealed to be the key determinants of the fungal communities in caves. Sample location and sampling distance from the entrance had more significant impacts on rock and sediment communities than on air and water assemblages. The fungal assemblages in air and water samples from the cave and outside cave environments were similar, while those of rock and sediment samples were significantly different. Main conclusions Our results indicate that sediment and water harboured higher fungal diversity than air and rock, and substrate and spatial variables are key determinants of fungal communities in caves.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 66%

Section: Introductionmentioning

confidence: 99%

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Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

Zhang

Cai

2019

Journal of Biogeography

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“…It can be explained by a diminution of rare species and a higher abundance of dominant species (Ager et al, ). This is compatible with fragmented data available from cave ecosystems, e.g., for culturable bacteria (Ikner et al, ) and fungi (Adetutu et al, ; Shapiro & Pringle, ), but not with DGGE findings on fungi (Adetutu et al, ) or the analysis of bleach treatment of cave walls (Pfendler et al, ). Here, the comparison of pristine and reference anthropized caves showed that anthropization was associated with reduced numbers of bacterial and archaeal OTUs, reduced estimated richness (Chao1) and diversity (Shannon) of archaea, and fewer arthropod predators especially Coleoptera (family Staphylinidae).…”

Section: Discussionsupporting

confidence: 86%

Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

et al. 2019

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Limestone areas across the world develop karstic caves, which are populated by a wide range of macro‐ and microorganisms. Many of these caves display Paleolithic art or outstanding speleothems, and in the last century they have been subjected to anthropization due to touristic management and intense human frequentation. Despite their cultural importance and associated conservation issues, the impact of anthropization on cave biodiversity is not known. Here, we show that anthropization is associated with specific cave biota modifications. We compared diversity in four pristine caves, four anthropized show caves, and the iconic Lascaux Cave with even stronger anthropization. The predominant microbial higher taxa were the same in all caves, but the most anthropized cave (Lascaux) was unique as it differed from the eight others by a higher proportion of Bacteroidetes bacteria and the absence of Euryarchaeota and Woesearchaeota archaea. Anthropization resulted in lower diversity and altered community structure for bacteria and archaea on cave walls, especially in Lascaux, but with a more limited effect on microeukaryotes and arthropods. Our findings fill a key gap in our understanding of the response of karstic communities to anthropization, by revealing that tourism‐related anthropization impacts on the prokaryotic microbiome rather than on eukaryotic residents, and that it shapes cave biota irrespective of cave natural features.

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“…The exogenous organic materials relocated in the show caves by tourists, support the growth of bacterial and fungal species alien to the cave community (Northup et al 2000, Chelius et al 2009, Jurado et al 2010, Saiz-Jimenez 2012, Pfendler et al 2018, often competing with the slow-growing oligotrophic native species (Vanderwolf et al 2013). The exogenous organic materials relocated in the show caves by tourists, support the growth of bacterial and fungal species alien to the cave community (Northup et al 2000, Chelius et al 2009, Jurado et al 2010, Saiz-Jimenez 2012, Pfendler et al 2018, often competing with the slow-growing oligotrophic native species (Vanderwolf et al 2013).…”

Section: Human-induced Ecological Impactsmentioning

confidence: 99%

Finding answers in the dark: caves as models in ecology fifty years after Poulson and White

2018

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The use of semi-isolated habitats such as oceanic islands, lakes and mountain summits as model systems has played a crucial role in the development of evolutionary and ecological theory. Soon after the discovery of life in caves, different pioneering authors similarly recognized the great potential of these peculiar habitats as biological model systems. In their 1969 paper in Science, 'The cave environment', Poulson and White discussed how caves can be used as natural laboratories in which to study the underlying principles governing the dynamics of more complex environments. Together with other seminal syntheses published at the time, this work contributed to establishing the conceptual foundation for expanding the scope and relevance of cave-based studies. Fifty years after, the aim of this review is to show why and how caves and other subterranean habitats can be used as eco-evolutionary laboratories. Recent advances and directions in different areas are provided, encompassing community ecology, trophicwebs and ecological networks, conservation biology, macroecology and climate change biology. Special emphasis is given to discuss how caves are only part of the extended network of fissures and cracks that permeate most substrates and, thus, their ecological role as habitat islands is critically discussed. Numerous studies have quantified the relative contribution of abiotic, biotic and historical factors in driving species distributions and community turnovers in space and time, from local to regional scales. Conversely, knowledge of macroecological patterns of subterranean organisms at a global scale remains largely elusive, due to major geographical and taxonomical biases. Also, knowledge regarding subterranean trophic webs and the effect of anthropogenic climate change on deep subterranean ecosystems is still limited. In these research fields, the extensive use of novel molecular and statistical tools may hold promise for quickly producing relevant information not accessible hitherto.

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Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data

Cited by 53 publications

References 57 publications

Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

Finding answers in the dark: caves as models in ecology fifty years after Poulson and White

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