Subterranean karst habitats, same as surface ones, include all groups of microorganisms, such as: archaea, bacteria, protozoa, algae and fungi like unicellular organisms.
Considering the absence of light in subterranean habitats, they are primarily inhabited by microorganisms that need no light (heterotrophic and chemotrophic organisms). Organisms that need light, such as algae and cyanobacteria, are found in entrance areas of caves where they build thin dark green layers that are easily seen by naked eye.
Archaea and bacteria are the simplest and smallest cave microorganisms (size smaller that 5 µm). They are present at all surfaces in caves such as bedrock, sediments, in all water masses, but also on the surface of animals (such as crustaceans). These organisms are at the bottom of the food web in subterranean habitats and they serve as food for other, larger microorganisms (such as protozoa) or small invertebrates which filter them from water (rotifers) or graze their biofilms (oligohaetes). Despite being the smallest inhabitants of the subterranean habitats, bacteria and archaea sometimes gather in colonies of great biomass. In that case they can be seen with the naked eye in the form of glittering white, greenish or golden layers over cave walls or in the form of fiber-like structures in subterranean water streams.
Protozoa, algae and fungi-like microorganisms are members of a group called protists (Protista). They are single-celled organisms with complex cell organization, which distinguishes them from bacteria and arhaea.
Protozoa that inhabit subterranean habitats are usually smaller than 100 µm and, together with bacteria, form a bottom of the food web. They are closely connected to water because it is a medium in which they live and use it for dispersion. In case of long droughts or absence of food, they transform into the cyst stage in which they can survive long periods of time. After the conditions become favorable again, protozoa return to active stages. So far, more than a hundred species from different systematic categories have been noted. There are species found in subterranean habitats that move freely on surfaces covered with water (amoeba Hartmannella vermiformis) or swim in water (ciliate Colpoda cucullus), some are attached on surfaces (ciliate Vorticella campanula), but there are also typical plankton species that float in water column (heliozoan Actinophrys sol). Some protozoa are attached on the cuticle of some subterranean crustaceans (ciliate Spelaeophrya troglocaridis) or on tubes of subterranean polychaete Marifugia cavatica (ciliate Diafolliculina hadzii). Some protozoa live as parasites in bats (flagelate Trypanosoma pipistrelli) and olm (alveolate protist Chloromyxum protei).
Fungi-like protists are very poorly researched in caves. They are found in substrates rich in organic matter such as bat’s guano.
In the Republic of Croatia, microorganisms are very poorly researched. The most studied are protozoa in Veternica Cave (Nature Park Medvednica), where more than fifty genera were noted from groups of flagellates, naked amoebas, testate amoebas, ciliates and heliozoans. The research of other freshwater, anhihaline and marine caves is also conducted, but at much lesser extent. Very complex bacterial colonies were found in fresh water streams of the already mentioned Veternica Cave.
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