Microbiology of extreme terrestrial and marine habitats in Italy

Our excursion took us to various extraordinary microbial habitats. Generally, microorganisms - bacteria, unicellular eukaryotes and (lower) fungi - are everywhere and important motors of biological cycles in all ecosystems. In every forest soil they are the main degraders of plant litter, they are present in all waterbodies and they are on our skin as well as in our intestine. Thus, microbial excursions can actually take place in front of and behind every door! We are primarily interested in special sites, where the "day-to-day" microbe is not abundant: in the deep underground, in hot springs and on rocky shores. In this context, Italy is particularly interesting, as it is much more geologically active than Central Europe.


On the northern foothills of the Apennine Mountains, the effects of the collision of two tectonic plates forms unusual sites. The pressure deep under ground leads to mobilization of water, methane gas and petroleum in deep reservoirs. Liquids, gas and clay move upwards and are expelled at the surface. This leads to the formation of small mud cones (Fig. 1). These mud volcanoes are cold - though the liquid is 60 °C hot in a depth of 2-3 km, it reaches the surface at ambient temperature. Methane, petroleum and dissolved salts allow unusual microbes to grow in the fluids. They degrade methane without oxygen - a process that has only recently been discovered and is still poorly understood.

Other interesting habitats are hot springs in Tuscany, which are located near the extinct volcano Monte Amiata. The volcano was last active 200,000 years ago, but its magma chamber is still heating up the groundwater. Enriched with dissolved calcium carbonate from sediments and with some hydrogen sulfide, hot water emerges from springs. At the surface, the dissolved calcium carbonate precipitates as calcareous sinter, which grows quickly and has been used since ancient times as an important building material (Fig. 2). The otherwise snow-white sinter terraces are populated with colorful microbes: blue-green cyanobacteria, greenish and brownish unicellular algae and yellow-stained sulfur oxidizers. In addition, there are many other organisms that live from these primary producers. At the spring sites, the water is 50-60 °C hot and only "thermophilic" species can live there.

Finally, we had a look at the shores of the Tyrrhenian sea: The ocean, of course, harbors a multitude of different habitats for microbes. They live in sediments or float in the free water, and many are associated with marine metazoa. One place was easy to reach for us, but with respect to microbes only accessible for specially adapted representatives: A rocky shoreline is an extreme place to live. Periodic dehydration and remoistening in the spray water zone, erosion and ultraviolet sunlight place special demands that not all microbes can cope with. Here, endolithic cyanobacteria are abundant; they actively drill down into the rock, which can be observed nicely at the rocky coast of the small island of Giglio (Fig. 3).

During the approximately 12-day excursion, we have not only visited these locations, we have also measured environmental parameters such as pH, oxygen and ion contents of spring water. Microscopic analysis in the field gave us a first short impression of the microbial diversity, but identification of the microbes requires molecular tools: During the excursion, we isolated the DNA from the samples that are used for metagenomic analysis to gain an overview of the composition of the entire biocoenosis.