This high abundance of ammonia-oxidizing archaea AOA is probably due to the high substrate affinity, which enables them to grow under far lower ammonia concentrations than other organisms [ 93 ]. The low availability of ammonia may be the reason for the higher abundance of AOA in this particular environment. Other factors such as moisture and temperature have also been demonstrated to influence the distribution and activity of Thaumarchaeota [ 20 , 94 ].
In this study we found that areas with a high presence of human associated bacterial 16S rRNA sequences SO2 show very little to no presence of archaeal or bacterial amoA gene sequences. It may be speculated that due to the increase of non-native microbes at this site, the native microbiome was displaced and eliminated by the invasive microbes.
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By doing so, cells would have been lysed, releasing DNA and other cellular constituents, which in turn can be used by the invasive species as nutrient source as described for extracellular DNA by Vorkapic et al. This may explain the low copy numbers recovered at SO2. This may be explained by the previously made statement that the regular impact on the microbiome by seasonal water flow may be responsible for this discrepancy.
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In this study we elucidated the microbiome of the Su Bentu Cave in Sardinia as well as the impact of exploration on the native microbiome. Similar to other investigated subterranean environments, a broad diversity of different microorganisms was recovered with Proteobacteria being the dominant phyla.
It can be concluded that infrequent exploration has a diminutive impact on the indigenous microbial population, compared to higher impacts for touristic caves [e. Further in-depth studies will certainly lead to the discovery of novel species with yet unknown traits for survival in low nutrient environments. The authors thank Oliena municipality for allowing access inside the Su Bentu Cave and Flavio Catte for his support given during the fieldwork.
XRF analyses were carried out by Prof. Enrico Dinelli University of Bologna. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Introduction Microorganisms inhabit a diverse number of extreme environments such as hot springs, glacial lakes and subterranean systems [ 1 — 4 ]. Material and methods The Su Bentu Cave Su Bentu Cave is located in the Supramonte karst massif Central-East Sardinia, Italy , a Mesozoic carbonate plateau, 9 km wide and 20 km long corresponding to an area of km 2 , topographically elevated over a Paleozoic crystalline basement.
Sampling sites The samples used in this analysis were collected in at 5 different remote areas of Su Bentu Cave, namely Ball Room, Shaft, and Water Tower, that only occasionally have been impacted by caver activity, as well as Piredda Hall which is close to a frequently used campsite during explorations and Chaos, a site close to the entrance were all explores have to pass to get into the cave.
Download: PPT. Microbiological sample collection Seven samples were taken during cave exploration at the previously described five sampling sites: Approximately 5 g of calcite raft, manganese oxide or moonmilk were sampled with a sterile spoon and filled into a 50 mL falcon tube containing 15 mL of RNAlater and mixed vigorously. Physico-chemical analysis of water Two water samples collected during the expedition display the same temperature, a quite similar specific electrical conductivity EC and total dissolved solid TDS , and an almost neutral pH Table 1.
Table 1. Water chemical parameters from representative areas in the cave. Table 2.
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Chemical composition XRF of the predominant cave sediments. Diversity and characteristics of the microbial community The microbial diversity of the Su Bentu Cave in Sardinia has been investigated at several different sampling locations Fig 1. Fig 3. Rarefaction analysis of the microbial communities at the different sampling points.
Table 3. Fig 4. Venn diagram showing the number of core, unique and shared species among the different sampling points.
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Fig 5. Relative class abundance of A the whole cave and B separated into the different sampling sites. Fig 6. Impact of human exploration on the microbial diversity in a hypogean system. Fig 7. Abundance of the bacterial and archaeal amoA genes. Discussion In this study we investigated the microbiome of the Su Bentu Cave, Sardinia by Illumina MiSeq analysis, focusing on the impact of human exploration on the indigenous microbial community and on the ammonia-oxidizing potential as an energy source. Calcite rafts SO1 The precipitation of CaCO 3 in cave pools occurs because such waters become saturated with respect to CaCO 3 due to the loss of CO 2 and evaporation at the air-water interface [ 67 , 68 ].
Ammonia-oxidizing potential The microbial oxidation of ammonia is a key process in the global cycling of nitrogen. Supporting information. S1 Table. Complete list of recovered phyla. S2 Table.
The core microbiome of the Su Bentu Cave. S3 Table. Complete list of recovered genera. S1 Fig. Full class abundance of the Su Bentu Cave. References 1. Life in extreme environments. Nature ; — Tomczyk-Zak K, and Zielenkiewicz U.
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Bacterial and archaeal diversity within the hot springs of Lake Magadi and little Magadi Lake in Kenya. Geomicrobiology in cave environments: past, current and future perspectives. J Cave Karst Stud. View Article Google Scholar 6. Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment. Chem Geol. View Article Google Scholar 8. Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy.
Environ Microbiol. Communities of Archaea and Bacteria in a subsurface radioactive thermal spring in the Austrian central alps, and evidence of ammonia-oxidizing Crenarchaeota. Appl Environ Microbiol.
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Antibiotic resistance is prevalent in an isolated cave microbiome. PLOS One ;7: e Barton HA. Starving artists: bacterial oligotrophic heterotrophy in caves.