The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co‐evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species‐specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of “core” microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co‐evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host‐microbiome association to originate and persist.
The potential of subterranean environments as models to address major evolutionary and ecological questions has been highlighted in the literature. They represent partially isolated, discrete units offering several replicates of the same evolutionary processes. Species occurrence data of these environments is abundant, although sparse in the literature or gathered in databases established according to regional, taxonomical, or ecological criteria. We here present a newly assembled dataset consisting of records of aquatic animals in all types of caves or wells from all over the world. Literature sources were gathered from Google Scholar by independently searching for each metazoan phylum/arthropod order, as well as the key words “cave”, “groundwater”, “well”, or “stygobite”, in English, Galician, Spanish, Portuguese, Catalonian, French, Italian, Hungarian, Greek, German, Polish, Russian, and Serbo-Croatian. The relevance of each source was confirmed after checking the title and the abstract. For each selected source, we examined its reference list in order to identify studies that were not published in journals indexed in the databases we searched. From the 6852 selected references, we manually extracted all records that concerned either occurrence of a species in a given geographical area or occurrence of any taxon in a particular cave or well. occurrence of a species in a given geographical area or occurrence of any taxon in a particular cave or well. Records were classified as primary or secondary, depending on whether they provided new information or referred to already publish records, allowing us to identify redundant information in posterior analyses. Information for each access point was organized in as a gazetteer, including synonym names, geographical, ecological, and geological information. Following this strategy, we have obtained 48,800 records (32,769, primary) from 1957 references checked so far. Most records are amongst fish and crustaceans. In contrast, few data exist for other groups that are comparatively diverse outside caves, such as Nematoda. Relevant information will be included in World Register of Marine Cave Species (Fig. 1).
We are ready for faunistic surveys of bdelloid rotifers through DNA barcoding: the example of Sphagnum bogs of the Swiss Jura MountainsThe identification of biological diversity through DNA barcoding and metabarcoding of the organisms living in the field has the potential to revolutionise the way biological surveys and monitoring are performed. Yet, we still do not know if the current representativeness of the reference database of DNA sequence data is sufficient to allow such approaches. Here, we show that, at least for bdelloid rotifers (Metazoa; Rotifera; Bdelloidea) in Europe, current knowledge is ripe to perform such surveys. We show the results of an exercise performed on bdelloid rotifers in Sphagnum bogs of the Swiss Jura Mountain. The results of DNA-based identifications were rather consistent with the morphology-based identifications, and the few cases of mismatch could be used as a cautionary tale to avoid potential misinterpretations of results. The mismatches were due to cases of the closest match not being genetically very close, and to the occurrence of cryptic species.
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