bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fascinating biology of stinky caves
Authors: Sarbu Serban 
Published: July 2022

The discovery of Movile Cave in 1986, similarly to the discovery of the deep-sea vents 9 years earlier, showed that, when redox interfaces are present in subsurface ecosystems, diverse and abundant biological communities can thrive based primarily on autochthonous food produced in situ by chemosynthesis. Additional caves, partially flooded by sulfidic water have been discovered, i.e. the Frasassi caves in Italy, Ein-Nur Cave and Ayyalon Cave in Israel, Melissotrypa Cave in Greece, Tashan Cave in Iran, caves in the Sharo-Argun Valley in the Caucasus Mountains, etc. All of these are inhabited by numerous endemic cave-adapted organisms present in dense populations sustained by a rich food base generated within the subterranean environment by microorganisms that use atmospheric oxygen to oxidize the reduced chemical compounds present in the water (H2S, NH4+, CH4). Stable isotope data has shown that the biological communities found in sulfidic caves are not dependent on carbon fixation in green plants that use light energy in the process of photosynthesis. Special adaptations have been identified in some of these inhabitants that allow them to cope with the adverse environmental conditions such as toxicity of H2S, hypoxia, and extreme pH values. Symbiotic associations between crustaceans, protozoa, and sulfide oxidizing bacteria were discovered in several sulfidic caves. New species of microorganisms have also been described from these unusual subsurface environments.
Unusual microbiomes have recently been discovered in dry caves that contain chemoclines between heavy volcanic gasses dominated by CO2, but also containing H2S and CH4, and atmospheric air that floats on top of the volcanic gas emissions. Unique sulfur mineralization, microbial biofilms containing new species of bacteria that thrive at extremely pH values, symbiotic relationships between bacteria and fungi have been discovered in Sulfur Cave in Romania, Bosoletto Cave in Italy, and Sousaki caves in Greece. The extreme life conditions encountered in these caves are of special interest to astrobiologists using these caves as a model for better understanding conditions that life may be present in on other planets and celestial bodies in our Solar System and beyond.
The morphology of the colonizers of the springs from the down-under
Authors: Biró Anna , Balázs Gergely , Fišer Žiga , Herczeg Gábor , Fišer Cene 
Published: July 2022

Transition from surface to subterranean environment generally results in easily detectable morphological changes, generally referred as troglomophism. Although the cave colonisation history of species can differ considerably, in certain cases there is a possibility to directly examine the cave-induced morphological and life history changes, as some of the troglobiont and stygobiont species still have closely related surface species. A less common and therefore less known phenomenon is the invasion in the opposite direction, when cave-adapted species establish stable populations (and later, new species) in surface or surface-connected (ecotonal) habitats. A great model taxon to study if morphological changes occur in such cases is the Niphargus genus, which primarily comprises subterranean species, although some species successfully colonised surface or ecotonal habitats.
To get insight of morphological changes and whether these changes were affected by sex, we measured 15 functional morphological traits on 488 individuals from both sex of eight Niphargus species, out of which four inhabit ecotonal (spring) habitats, while the other four are exclusively subterranean. We analysed our data trait-by-trait with linear mixed models. We found that colonising the “new” habitat did not demonstrably affect morphology. In contrast habitat dependent sexual dimorphism was found in case of the 2nd gnathopods’ coxa. Besides the aforementioned habitat dependent sexual dimorphism, we found sexual dimorphism in case of 11 out of the 15 traits. Based on our result we can assume that morphological changes might happen in the course of the colonisation of the novel habitat, but they are not as unambiguous as when surface species colonise caves. It is also possible that although we consider springs as ecotone or even surface habitats, they might be feasible for subterranean species without striking morphological changes as they do not meet selection forces strikingly different from those present in caves.
Preliminary study on differences characterizes the populations of olm (Proteus anguinus) in cave and those found in epigean environment
Authors: Barzaghi Benedetta , Ficetola Francesco Gentile , Mauri Edgardo , Restaino Marco , Lombardi Bianca , Manenti Raoul 
Published: July 2022

The olm (Proteus anguinus) is considered the most representative example of all the stygobiont fauna. Nevertheless, it is also reported in some spring habitats of Friuli Venezia Giulia (North-eastern Italy). Springs are intriguing habitats that border two strongly distinct environments: surface and underground. They may provide distinct environmental pressures to stygobiont animals promoting new adaptations.
The aim of this study is to verify if there are differences in the structural morphology of the head and in the presence of melanin in the skin between the olms that are found in caves compared to the individuals found in the external environment.
During 2021, 28 olms, 18 from underground habitats and 10 from external sites, were photographed in standard conditions with a metric reference. For each individual, only the cephalic region has been considered. The pictures were processed using TPSdig software. For each picture we placed 2 landmark homologues, matching the emergence of the gills branches, and 48 semi-landmark to define the contour of the head. With regard to melanin 2 mm of skin were removed from the tail of the olm and analyzed through a spectrophotometer. The results indicate a significant effect of the environment on the shape of the olm’s head, in fact the shape of the head appears more elongated in the front and narrower in the parietal region in the olms coming from the hypogean environment. In addition, the olms that use the epigean environment show higher melanin levels in their skin.
These findings provide a first evidence of differences occurring between olm populations/sub-populations living in caves and those exploiting surface habitats.
Different components of interconnected karst environment select for highly distinct microbial communities
Authors: Singh Anusha , Shabarova Tanja , Bulzu Paul 
Published: July 2022

Karst environments, formed by dissolution of rocks, present a unique opportunity to study groundwater and surface water as a single dynamic system. We aimed to explore the hydrological connections and identify shared microbiome between different components of this complex landscape (terrestrial, surface-subsurface freshwater networks and two different lake strata) on example of karst landscape at north shore of Lake Thun (CH).
52 samples from soil and 87 from the freshwater network were collected during low hydrological conditions. Additionally, 43 samples from 13 different lakes across Europe were included in the analysis. A 16S rRNA gene amplicon analysis revealed highly homogenous lake communities dominated by typical lake microbes represented by members of Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. On the contrary, communities in soils and surface and subsurface water were observed to be highly heterogenous within the karst landscapes. Soil samples built two robust groups that corresponded to alkaline and acidic pH values associated with two types of bedrocks. Alkaline soils had higher abundance of Gammaproteobacteria and Alphaproteobacteria, while acidic soils were dominated by Acidobacteria. Alkaline cluster was better connected with aquatic environments and shared genotypes from the families Nitrosomonadaceae and Nitrospiraceae with cave sediments and lake hypolimnia, that implied ammonia and nitrite oxidation as important chemotrophic processes in light depleted environments. Rhodoferax, Limnohabitans and Sediminibacterium were shared within subsurface network and lakes. Single Rhodoferax genotype was detected in all aquatic environments. Additionally, we observed that lineages from the families Pirellulaceae and Gemmataceae (phylum Planctomycetota) were alternatively distributed in both soil clusters and lakes. A similar pattern was observed in subsurface aquatic components and deeper lake strata within family Methylophilaceae, where Methylotenera was extensively replaced by Methylopumilus. This indicates that despite high hydrological connectedness between different karst landscape components, deterministic selective factors seem to prevail in the community assemblies.
Insights into the Eucyclops graeteri species complex (Copepoda, Cyclopidae) — the case of sulphidic groundwaters of Mangalia (Southern Dobrogea, Romania)
Authors: Pop Maria , Ștefan Andrei , Boancă Filip , Stoch Fabio , Iepure Sanda 
Published: July 2022

Members of the Eucyclops graeteri species complex are widely distributed in European groundwaters and share some morphocharacters such as:

a long aesthetasc on the ninth segment of female antennula,

short or very reduced spinule row ("serra") on furcal rami,

lateral hairiness of 5th thoracic somite strongly reduced, and

few or no hairs on the distal margin of the intercoxal sclerite of 4th legs pair.

a long aesthetasc on the ninth segment of female antennula,
short or very reduced spinule row ("serra") on furcal rami,
lateral hairiness of 5th thoracic somite strongly reduced, and
few or no hairs on the distal margin of the intercoxal sclerite of 4th legs pair.
All these characters are subject to strong selective pressure in the underground environment; therefore, the study of molecular markers is needed to better define the taxonomy and phylogeny of this species group. The Southern Dobrogea region in Romania conceals dark, isolated, and sulfide-rich aquifers, accessible through artificial wells, springs, and the Movile Cave. The chemoautotrophically-based Movile Cave hosts a member of the E. graeteri complex, described several years ago as a subspecies (E. graeteri scythicus Plesa, 1989). The morphological and molecular analyses performed on specimens of this species complex collected from Southern Dobrogea revealed new records for E. graeteri scythicus both in sulfidic and non-sulfidic artificial wells dug near the cave as well as a species putatively new to science collected in three sulfidic wells from Mangalia. Mitochondrial markers allocated the Movile Cave population in a distinct clade within the genus Eucyclops, Eucyclops serrulatus s.l. being the closest taxon. The putative new species belongs to a different clade within the subfamily Eucyclopinae, raising doubts on the monophyly of this species complex. Furthermore, our investigations revealed the occurrence of ectosymbiont sulfur-oxidizing Thiothrix bacteria associated with E. graeteri scythicus suggesting that this putative symbiosis could allow this taxon to better cope with sulphidic-rich environments. These unique sulfidic groundwater environments therefore provide an interesting model system in which to study the taxonomy of copepods and their adaptation to very harsh environmental conditions.
The genus Protopholeuon (Coleoptera, Leptodirini): distribution, morphological, ultratructural and genetic details
Authors: Sitar Cristian , Bucur Ruxandra , Kenesz Marius , Moldovan Oana Teodora 
Published: July 2022

Protopholeuon is a monospecific genus of Leptodirini, endemic to Romania, represented by Protopholeuon hungaricum, described incompletely by Csiki in 1904. In 1923, René Jeannel published a more comprehensive morphological description of the species, along with the first drawing of male genitalia.
The type locality of the species is Lucia Cave, in the Metaliferi Mountains (Apuseni Mountains). This was the only locality where the species was found and collected. In the last decade, representatives of the genus Protopholeon were found in other caves of the Metaliferi Mountains. These caves are: Grohot, Izbucul Topliței, Ponor, Rusești, Hodobana, Cizmei, Urșilor Bulzești. The aerial distance between Lucia Cave and the newly explored caves is about 20 km. The patchy geology and hydrology of the area can act as natural barriers that shape the species' geographic distribution and enhance the speciation process.
We provide morphometric information for Protopholeuon specimens obtained from 80 individuals. We also present the pictures of Protopholeuon with morphological and ultrastructural details (SEM microscopy) for head, mandibles, antennae, elytra surface and aedeagus. All this completes the morphological description made in 1923 by Jeannel.
We present the first data on the molecular analysis of a mitochondrial COI fragment on Protopholeuon all the mentioned caves. For every cave, we analyzed 2-3 specimens. Our working hypothesis was that considering the distribution of caves, P. hungaricum from Lucia Cave represents a distinct phylogenetic unit from the other sampled caves of the Metaliferi Mountains. As an outgroup for rooting the phylogenetic tree, we used sequences from Pholeuon, another genus of endemic Romanian Leptodirini.
The molecular analysis revealed a unique clade for all samples from Metaliferi Mountains. Moreover, a single clade is built by all Metaliferi haplotypes, except Lucia Cave, with a high bootstrap value (85%). The genetic distance between ingroup and outgroup samples is 7-8%, while between the Lucia haplotype and the other haplotypes from Metaliferi Mountain the range is 3-4%, which agrees with other results from the group of Romanian Leptodirini. The distances between Metaliferi Mountain haplotypes (except Lucia Cave) are 0.1-2.8%, grouping in two distinct clades, with high statistical values. Still, the taxonomic status of samples from the Metaliferi Mountains should be further investigated by corroborating morphologic and genetic data.
IUCN red-listing of subterranean invertebrates: problems, gaps and the future
Authors: Deharveng Louis , Komericki Ana , Khela Sonia 
Published: July 2022

Red-listing is a widely used approach to globally evaluate the threats that affect a species, according to a set of standardized criteria. The IUCN Red List of Threatened Species is the world's most comprehensive inventory of the global conservation status of species. It is an international reference in this field, and a powerful tool for conservation of endangered species, sites and habitats.
A number of subterranean organisms of various taxonomical groups have been assessed from a few decades, and are currently being assessed, revealing serious difficulties and uncertainties linked to the special characteristics of subterranean ecosystems and species. The most critical problems, that are linked to distribution, dispersion, life cycle and sensitivity to disturbance, and some ways to overcome them, are discussed in this paper.
Partly linked to this, redlisting of subterranean species has so far achieved moderate results with regard to the diversity and vulnerability of subterranean species - with the well-known exception of bats. Data drawn from IUCN online database of redlsted species reveals that subterranean invertebrates are hugely under-covered at geographical and taxonomic levels. Moreover, among red-listed species that are connected to subterranean habitats, most are stygophiles and troglophiles, i.e. not obligate cave dwellers. In contrast, very few of the species strictly linked to subterranean life (stygobionts and troglobionts) have been red-listed so far, in spite of the exceptional proneness to endemicity of subterranean invertebrate groups.
On an other hand, assessments are extremely uneven across countries and across taxa. Many regions with significant cave fauna do not have any assessed subterranean species. The richest countries in subterranean diversity are not those which have the highest number of assessed species. The zoological invertebrate groups that dominate cave fauna in diversity (beetles, springtails, microcrustacea...) have contrasted proportion of redlisted species: higher for snails, very low for microcrustaceans, beetles and springtails, with rare local exceptions.
Assessment difficulties underlined above, low coverage of cave fauna in available assessments, limited progress in number of red-listed species in the face of the high number of concerned species, and the limited human resources to do the job led us to favour a more pragmatic approach to subterranean invertebrates red-listing for the coming years. Really threatened subterranean species are actually not numerous, because subterranean habitats are protected from most critical disturbance that devastate so many surface habitats. The aim will be therefore to focus on the most threatened species and sites in the world, with a particular attention on mining, water pollution and large scale surface habitats destruction.
A Feulgen glimpse into genome evolution during range expansion: a case study of the subterranean amphipod Niphargus schellenbergi
Authors: M.Tawfeeq Mohammed , Weber Dieter , Flot Jean-François 
Published: July 2022

In 1923, Robert Feulgen designed a quantitative approach to measure the relative DNA content of a species (its so-called “C-value”, which is defined as half of the DNA content of a somatic cell and is expressed in pg). The Feulgen approach has several advantages: it can be used on ethanol-preserved samples, it is relatively inexpensive, and it does not require sophisticated equipment (Hardie et al. 2002, Jeffery and Gregory 2014, Kasten 2003). Gathering DNA content information is a key preliminary step for whole-genome sequencing of non-model species and also yield important information for ecological and evolutionary studies as well as for conservation (Jeffery et al. 2013), since genome size has been shown to be strongly correlated to extinction risk in animals and plants (Vinogradov 2004, Vinogradov 2003).
Among invertebrates, Niphargidae is among the largest families of freshwater subterranean amphipods in the world, and more than 450 niphargid species have been described (Horton et al. 2021). Thus, it is considered an ideal model for evolutionary and ecological studies. Using a new, improved Feulgen protocol, we generated novel genome size estimates for 26 samples of Niphargus schellenbergi collected from central and western European niphargids. The obtained C-values ranged from 2.75 to 5.25 pg. Such a two-fold intraspecific variation is unusual but not unheard of: it occurs also in the monogonont rotifer Brachionus asplanchnoidis (Stelzer et al. 2021). Further research will be required to find out the mechanisms responsible for this variation, which may result from copy-number variation, polyploidy and/or various amounts of transposable elements.
Overcoming shortfalls and impediments in subterranean biology: a challenge for the future
Authors: Stoch Fabio , Flot Jean-François 
Published: July 2022

Since the discovery and description of the first specialized cave species, subterranean fauna stimulated the scientific research of several generations of speleobiologists especially after the publication of Racovitza's classification of cave species, which is still used today, amended for non-karstic areas and groundwaters. More than 28,000 obligate subterranean species are known worldwide; however, these figures are likely to be underestimated since species richness is highly correlated with research effort (Stoch and Galassi 2010). Subterranean ecosystems are very rich in strict endemic species and taxonomic efforts are still quite low (i.e., the so-called "taxonomic impediment"), while several environments are very difficult to be explored (i.e., the "Racovitzan impediment: Ficetola et al. 2018).
Furthermore, several paradigms were debated for years. Albeit constrasting hypotheses were conceived to explain the colonization of subsurface habitats, their importance is still debated (i.e., climate relicts vs. adaptive shift in colonization and speciation, dispersal vs. vicariance in shaping distributional patterns, and selective vs. neutral hypotheses in explaining regressive evolution). Moreover, the paradigm of a "truncated functional diversity" of subterranean ecosystems (Gibert and Deharveng 2002) lasted for years but was recently challenged by the discovery of chemoautotrophic ecosystems in hypogenic and anchialine caves, and the recognition that caves are not isolated environments, but they are highly interconnected with surface ecosystems. The increased importance of their conservation (like in the case of GDEs, Groundwater Dependent Ecosystems) was recently recognized, together with their provision of important ecosystem services (Boulton 2020).
A deeper knowledge is required to assess biodiversity hotspots as well as to plan efficient monitoring surveys (Mammola et al. 2020). In the last decades, a growing amount of molecular data has been obtained for subterranean species, allowing some of the classical debates on colonization, evolution, and dispersal to be revisited (Bauzà-Ribot et al. 2012); moreover, novel promising techniques like metabarcoding and environmental DNA were applied in field surveys and monitoring efforts.
Unfortunately, after more than one century of research in subterranean biology, large gaps remain in our knowledge of phylogeny, richness, and distribution of subterranean fauna (formalized in the so-called Darwinian, Linnean and Wallacean shortfalls), preventing the definition of large-scale sound management and protection plans. It is proposed that data from recent biomolecular techniques coupled with remotely sensed data may enhance biodiversity mapping and conservation and are promising approaches to fill our knowledge gaps. Perhaps this is the greatest challenge that tomorrow's subterranean biologists will face.
Les demandeurs d’asile et les réfugiés en France et en Allemagne depuis 2015
Authors: Aulanier Audran , Bartel Anja 
Published: July 2022

Si l’Allemagne fait souvent figure de modèle dans le débat public et politique français sur les politiques d’accueil, cet intérêt n’est guère réciproque. À cela s’ajoute la quasi-absence de travaux scientifiques comparatifs sur les politiques d’accueil à l’égard des personnes en exil. Pour autant, comme le montre cette introduction à partir d’exemples relatifs aux systèmes de répartition des demandeurs d’asile, à l’organisation et aux résultats de la procédure d’asile, ainsi qu’aux différentes conceptions nationales de l’intégration, ces politiques, au-delà de leurs convergences, restent marquées par de fortes différences. Celles-ci invitent à enquêter sur les effets de ces politiques en France et en Allemagne en partant « du bas », à partir d’enquêtes empiriques mettant au centre les expériences de différents acteurs, tels que les villes, les associations ou les personnes en exil.