Abstract
The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments). On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk—a hydrated calcium-magnesium carbonate speleothem—can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains). Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite–located 500 meters deep into the cave—revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a highly specialized microbiome, which is perfectly adapted to survive and thrive in an environment with low nutrient availability.
Highlights
Microorganisms inhabit a diverse number of extreme environments such as hot springs, glacial lakes and subterranean systems [1,2,3,4]
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
Subterranean ecosystems are distinguished by a variety of physical and chemical parameters
Summary
Microorganisms inhabit a diverse number of extreme environments such as hot springs, glacial lakes and subterranean systems [1,2,3,4] Due to their subsurface nature, being hosted deep underground, and to the lack of sunlight, caves are nutrient depleted environments where the levels of available organic carbon to support heterotrophic microbial growth are significantly lower than in terrestrial surface ecosystems [5]. Representatives of the phylum Proteobacteria are prevalent and abundant in caves such as the Tito Bustillo cave in Spain [15] or the karstic Herrenberg cave in Germany [16] This group represents the dominant phylum in biofilms, matrix-enclosed bacterial populations adherent to each other and the surface [17], which have been studied in serval other caves such as the Grotta de Fiume ([8]), karst systems in Slovenia [18] and the Lower Kane Cave in Wyoming [19]
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