Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia inducible genes

Dark caves lacking primary productivity can expose subterranean animals to hypoxia. We used the surface-dwelling (surface fish) and cave-dwelling (cavefish) morphs of Astyanax mexicanus as a model for understanding the mechanisms of hypoxia tolerance in the cave environment. Primitive hematopoiesis, which is restricted to the posterior lateral mesoderm in other teleosts, also occurs in the anterior lateral mesoderm in Astyanax, potentially pre-adapting surface fish for hypoxic cave colonization. Cavefish have enlarged both hematopoietic domains and develop more erythrocytes than surface fish, which are required for normal development in both morphs. Laboratory induced hypoxia suppresses growth in surface fish but not in cavefish. Both morphs respond to hypoxia by overexpressing hypoxia-inducible factor 1 (hif1) pathway genes, and some hif1 genes are constitutively upregulated in normoxic cavefish to similar levels as in hypoxic surface fish. We conclude that cavefish cope with hypoxia by increasing erythrocyte development and constitutive hif1 gene overexpression.

Evaluating carbonate dissolution and precipitation in a short time-frame using SEM: techniques and preliminary results from Postojna Cave, Slovenia

Carbonate dissolution and precipitation are important geological processes whose rates often require quantification. In natural settings, these processes may be taking place at a slow rate, and thus, it may not be easily visible which of these processes is occurring. Alternatively, if the effects of precipitation/dissolution are visible, it may not be clear if they are still underway or an artefact of past conditions. Moreover, these two opposing processes may flip states depending on the environmental conditions, such as, on a seasonal basis. Here, we present the technical details and preliminary results of a method using carbonate tablets and Scanning Electron Microscopy (SEM) to evaluate which process (carbonate dissolution or precipitation) is occurring, using as an example, a cave environment. Our method involves making tablets by encasing blocks of carbonate rock into resin and polishing these to form a completely flat and smooth “zero surface”. These tablets are observed under SEM in exactly the same points both before and after exposure to the field environment, using a system of marking lines at specific locations on the resin. Our results show significant differences in the before and after images of the tablet surface after just six weeks in the cave. Furthermore, the use of the insoluble resin zero surface permits a comparison of the starting height with the new dissolved/precipitated surface that can be used to quantitatively estimate the rate of dissolution/precipitation happening at a field location in a relatively short time-frame (weeks/months). This method could be used in numerous natural and industrial settings to identify these processes that can be caused purely geochemically, but also through microbialmediation and physical weathering.

First draft Genome of Loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the Evolution of Cavefish

BackgroundLoaches from the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth, and some species of loach inhabit the underground drainage. The genus Oreonectes with 18 currently recognized loach species represent the three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable research resource of the evolution of cavefishes.ResultWe assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. The genome assembly contains 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. Meanwhile,we found that dozens of genes related to eye development and melanogenesis were pseudogenised during the evolutionary process in cave environment, providing novel insights into complex phenotypic adaptations of animals in specific environment. ConclusionHere we report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. This genome assembly will contribute to the study of the evolution and adaptation of cavefishes within Oreonectes and beyond (Cobitidea) and provid valuable genomic resources for studies on the evolutionary history of the rapid speciation processes of family Nemacheilidae.

Metataxonomic Analysis of Bacteria Entrapped in a Stalactite’s Core and Their Possible Environmental Origins

Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.

Adapting to novel environments together: evolutionary and ecological correlates of the bacterial microbiome of the worlds largest cavefish diversification

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the hosts physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A to D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for six months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at clade level, with the most geographically distant clades (A and D) being the most distinct, and two geographically overlapping clades (B and C) being similar. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters was. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying adaptability and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group closely resembled that of other teleost fishes. Our results suggest that divergent selection giving rise to evolutionary novelties also includes the microbiome of these fishes, which provides a functional advantage for life in the resource-depleted cave environment.

Earthquake effects and insights on fault activity at the Beatrice Cenci cave (Abruzzo, Central Apennines)

he focus of this study is the analysis of a cave in Central Italy, the Beatrice Cenci cave, in order to point out and constrain evidence of possible past earthquakes and of fault activity in the area. We performed a survey of seismic related damages within the cave. This included the analysis of broken/collapsed speleothems, the recognition of structural collapse, of tilting/growth alteration in the speleothems, and the mapping of fractures, joints and/or faults. To timely set the occurrence of the recognized damage, organic sediments were dated with 14C radiocarbon method. The results merged toward the recognition of two distinct seismic shaking events affecting the cave environment, one older than 30 kyr and another around 7 kyr. The deformation observed within the cave led us to the hypothesis that the events of damage were possibly linked to the activity of the regional tectonic lineament that crosses the cave, i.e., the Liri normal fault. The morphology and the evolution of the cave appear controlled by the fault zone. These speleoseismological results provided a new contribution on the knowledge of the past activity of the Liri fault and on the earthquake history of this sector of Central Apennines.

Morphological Adaptation of Cave-Dwelling Ground Beetles in China Revealed by Geometric Morphometry (Coleoptera, Carabidae, Trechini)

Cave-dwelling ground beetles in China represent the most impressive specific diversity and morphological adaptations of the cavernicolous ground beetles in the world, but they have not been systematically examined in quantitative terms. The present study focuses on the application of geometric morphological methods to address the morphological adaptations of the tribe Trechini, the most representative group in China. We have employed a geometric morphometry analysis of the head, pronotum, and elytra of 53 genera of Trechini, including 132 hypogean and 8 epigean species. Our results showed that the overall morphological variation of cave carabids has gradually specialized from an anophthalmic to semi-aphaenopsian to aphaenopsian type. There were extremely significant differences (p < 0.01) among four different adaptive types including aphaenopsian, semi-aphaenopsian, anophthalmic, and surface-dwelling Trechini when their adaptability to a cave environment was used as the basis for grouping. Furthermore, there were differences in the phenotypic tree of the head, pronotum, and elytra, and an integrated morphology. To the best of our knowledge, this is the first report on the analysis of the head, pronotum, and elytra of four different adaptive types of ground beetles in order to clarify the morphological adaptations of cavernicolous carabids to the cave environment.

Finely dispersed salt particles morphometric properties obtained by carnallite solutions spray drying

Currently, there is no consensus on the salt caves aero ionic environment effects mechanism on the human body, however, there is physiotherapy a separate type, based on such exposure health-improving effect, known as speleotherapy. To recreate the salt cave environment aero ionic composition, a halo chamber is used. To reduce their cost, recreating the air environment methods by contacting flowing air means with carnallite rock finely dispersed powder and dry and wet aerosols generators have been developed. When implementing these methods, both the powder obtained directly by crushing the rock and the powder obtained by salt solutions evaporation drying can be used. The study aim is to reveal finely dispersed salt particles morphometric properties obtained by carnallite solutions spray drying based on different dispersion raw materials. It has been established fine salt particles those morphometric properties obtained by spray drying of carnallite solutions based on different dispersion raw materials differ in average size, sphericity factor, topography character and chemical composition. Particles formed by solution evaporation on the macro disperse raw materials (3-5 mm) basis have larger size, smaller fractional range, more compact shape and relief characterized by multifractality. At the same time, solution-based particles from macro disperse raw materials contain more impurities. Particles a distinguishing characteristic from solution-based lumpy raw materials is the potassium cluster distribution on the surface.

Nyitni vagy nem nyitni? – Pilisi barlangok szellőzöttsége a geokémiai adatok tükrében

Speleothem formations are one of the most important and informative objects in paleoclimatological research. However, in order to interpret the data that reflect environmental conditions, we have to know the operation of the given cave, and it should be determined how the composition of the carbonate formed at the given site is related to the changes in the environmental parameters. The study presents the results of stable isotope geochemical analysis of speleothem formations and carbonate precipitated on glass plates collected in the Vacska Cave (Pilis Hills). The youngest layer of carbonate formations, formed in the last 1-2 decades, shows an isotope fractionation sign indicating strong ventilation, with the exception of a single site farthest from the entrance to the cave. The isotope shift was also accompanied by a change in carbonate fabric. Preceding the fabric change, the carbonate of the speleothem formations did not show ventilation-related shifts in the isotope compositions, suggesting that the exploration and opening of the cave areas may have caused the change. Based on this, we recommend the installation of local closures in the Vacska Cave and in the entire Ariadne cave system. The study provides a good example of how the results of basic research can be utilized in practical environmental protection, in the preservation of a strictly protected cave environment.

Morpho-Mineralogical and Bio-Geochemical Description of Cave Manganese Stromatolite-Like Patinas (Grotta del Cervo, Central Italy) and Hints on Their Paleohydrological-Driven Genesis

Caves are dark subsurface environments with relatively constant temperatures that allow studying bio-mineralization processes and paleoenvironmental or climate changes in optimal conditions. In the extreme and oligotrophic cave environment, manganese patinas having stromatolite-like features are uncommon. Here we provide the first detailed mineralogical, geochemical, and microbiological investigation of fine-grained and poorly crystalline MnFe stromatolite-like wall patinas formed in a deep-cave environment in Italy. These mineralizations, about 3 mm thick, consist of an alternation of Mn-layers and Fe-lenses. We show that the microbial communities' composition is dominated by Mn-oxidizing bacteria, such as Bacillus, Flavobacterium, and Pseudomonas. Our multidisciplinary investigation, integrating data from different analytical techniques (i.e., optical microscopy, SEM-EDS, μXRF, XRPD, FT-IR, Raman spectroscopy, and DNA sequencing), revealed peculiar chemical, mineralogical, and biological features: 1) A cyclical oscillation of Mn and Fe along the growth of the patinas. We propose that this oscillation represents the shift between oxic and suboxic conditions related to different phases occurring during paleo-flood events; 2) A typical spatial distribution of mineralogy and oxidation state of Mn, bacterial imprints, detrital content, and stromatolite-like morphologies along the Mn-layers. We propose that this distribution is controlled by the local hydraulic regime of the paleo-floods, which, in turn, is directly related to the morphology of the wall surface. Under less turbulent conditions, the combination of clay mineral catalysis and biological oxidation produced vernadite, a poor-crystalline phyllomanganate with a low average oxidation state of Mn, and branched columnar stromatolite-like morphologies. On the other hand, under more turbulent conditions, the sedimentation of clay minerals and microbial communities' development are both inhibited. In this local environment, a lower oxidation rate of Mn2+ favored the formation of todorokite and/or ranciéite, two compounds with a high average oxidation state of Mn, and flat-laminated or columnar stromatolite-like morphologies.