The ticking clock in the dark: Review of biological rhythms in cave invertebrates

Circadian clocks, internal mechanisms that generate 24-hour rhythms, play a crucial role in coordinating biological events with day-night cycles. In light-deprived environments such as caves, species, particularly isolated obligatory troglobites, may exhibit evolutionary adaptations in biological rhythms due to light exposure. To explore rhythm expression in these settings, we conducted a comprehensive literature review on invertebrate chronobiology in global subterranean ecosystems, analyzing 44 selected studies out of over 480 identified as of September 2023. These studies revealed significant taxonomic diversity, primarily among terrestrial species like Coleoptera, with research concentrated in the United States, Italy, France, Australia, and Brazil, and a notable gap in African records. Troglobite species displayed a higher incidence of aperiodic behavior, while troglophiles showed a robust association with rhythm expression. Locomotor activity was the most studied aspect (>60%). However, approximately 4% of studies lacked information on periodicity or rhythm asynchrony, and limited research under constant light conditions hindered definitive conclusions. This review underscores the need to expand chronobiological research globally, encompassing diverse geographical regions and taxa, to deepen our understanding of biological rhythms in subterranean species. Such insights are crucial for preserving the resilience of subsurface ecosystems facing threats like climate change and habitat loss.

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

Behavioral responses of cave-roosting bats to artificial light of different spectra and intensities: Implications for lighting management strategy

Artificial light at night has become an emerging environmental pollutant, posing a serious threat to biodiversity. Cave-roosting animals are vulnerable to light pollution due to long-term adaptation to nocturnal niches, and the problem is especially severe in the context of cave tourism and limestone mining. Mitigating the adverse impacts of artificial light on cave-dwelling animals presents a challenge. This study aimed to assess the relative contributions of spectral parameters and light intensity to the emergence behavior of nine cave-roosting bat species: Rhinolophus macrotis, Rhinolophus pearsonii, Rhinolophus rex, Rhinolophus pusillus, Rhinolophus siamensis, Rhinolophus sinicus, Hipposideros armiger, Myotis davidii, and Miniopterus fuliginosus. We manipulated light spectra and intensities through light-emitting diode (LED) lighting and gel filters at the entrance of bat roost. We monitored nightly passes per species to quantify bat emergence under the dark control and ten lighting conditions (blue, green, yellow, red, and white light at high and low intensities) using ultrasonic recording. Our analyses showed that the number of bat passes tended to be reduced in the presence of white, green, and yellow light, independent of light intensity. In contrast, the number of bat passes showed no pronounced differences under the dark control, blue light, and red light. The number of bat passes was primarily affected by LED light's blue component, red component, peak wavelength, and half-width instead of light intensity. These results demonstrate that spectral parameters of LED light can significantly affect emergence behavior of cave-dwelling bats. Our findings highlight the importance of manipulating light colors to reduce the negative impacts of light pollution on cave-roosting bats as a function of their spectral sensitivity. We recommend the use of gel filters to manage existing artificial lighting systems at the entrance of bat-inhabited caves.

Quantity and spatial distribution of earth-air activity in Cave 108 of the Dunhuang Mogao Grottoes

Monitoring of earth-air humidity in soil has revealed extensive rising/falling activity on the land. Alternation of dry and wet air is the main root cause deterioration in cave wall paintings. However, the quantity and spatial distribution of earth-air activity in caves remain unclear. This study used air flowmeters to monitor the earth-air outflow at 136 points on the west, south, and north walls of Cave 108 in the Dunhuang Mogao Grottoes, and to determine its spatial distribution. Results showed that under the influence of atmospheric fluctuation, there is frequent air exchange between the atmosphere and the earth-air, and that the daily outflow of earth-air from Cave 108 is 50.893 m3/d. Earth-air flux is negatively correlated with atmospheric pressure, and the fluctuation of atmospheric pressure is the main driving force of earth-air activity. The average outflow of earth-air from the ground of Cave 108 is 0.109 L/(min·m2). Apart from that, the overall spatial distribution of earth-air quantity showed the following pattern: ground > west wall > north wall > south wall. What's more, the outflow of earth-air is inversely proportional to the wall height, while proportional to the depth of the cave embedded in the cliff. In such case, sealing the cave floor with concrete will heighten earth-air flow on the walls, thereby quickening the deterioration process of wall paintings. This study unveiled the deterioration mechanism of wall paintings in the context of earth-air conditions, thus establishing a foundation for the scientific protection of wall paintings.

The genus Inversotyphlus Strasser, 1962, stat. nov. and Inversotyphlusammirandus sp. nov., a new bizarre, highly modified troglobiotic millipede (Diplopoda, Julida, Julidae) from Albania, Balkan Peninsula

Inversotyphlus Strasser, 1962, stat. nov. is raised to the genus level and a new hydrophilous species, Inversotyphlusammirandussp. nov., is described from the second deepest pit in Albania. This species is characterized by a highly modified head and body for a presumably semiaquatic or hygropetric life and filtering diet. It is by far the most bizarrely modified cave-dwelling julid known. The new species is diagnosed, described in detail, and richly illustrated. Besides I.ammirandussp. nov., the genus Inversotyphlusstat. nov. includes six species: I.clavatus (Antić, 2018), comb. nov., I.edentulus (Attems, 1951), comb. nov., I.gellianae (Makarov & Rađa, 2006), comb. nov., I.gracilis (Antić, 2018), comb. nov., I.lobifer (Attems, 1951), comb. nov., and I.opisthonodus (Antić, 2018) comb. nov. The subgenus Attemsotyphlussyn. nov. is here considered as a junior subjective synonym of the genus Inversotyphlusstat. nov. Notes are given on the habitat of I.ammirandussp. nov., the taxonomy of the tribe Typhloiulini and the genus Inversotyphlusstat. nov., and adaptive modifications of the mouthparts.

Middle and Upper Paleolithic occupations of Fumane Cave (Italy): a geoarchaeological investigation of the anthropogenic features

Here we present the results of a microcontextual analysis of purported combustion features recovered from Middle and Upper Paleolithic occupations at the cave site of Fumane, Italy. Our analyses, which integrate micromorphology with organic petrology, show that only a few of the features represent primary, intact hearths; some of them show evidence for various phases of anthropogenic reworking, either through trampling or sweeping and dumping. Several of the features are multi-layered and reflect a complex formation history of various activities related to combustion and site maintenance. Many appear to be the remnants of occupation horizons only partially preserved and peripherally related to combustion. Within several of the intact hearths from the Mousterian, we were able to identify variable fuel sources in different features, implying a degree of flexibility in the fuel-selection strategies of the Neanderthal occupants of Fumane. In this study we design a classification system of the anthropogenic features and also conduct a spatial analysis, through which we can infer diachronic patterns in the frequency and intensity of site occupation and the spatial distribution of activities. We note a decrease in frequency of combustion features throughout the Mousterian which continues into the Uluzzian. The features associated with the Protoaurignacian occupation, in contrast with those from the Mousterian, are multi-layered and well-defined. We argue that these trends, which correspond with other trends in artefact frequency, imply changes in the settlement dynamics of the site during the transition from the last Neanderthal occupation of the cave to the arrival of modern humans.

Speleomycology of Air in Stopića Cave (Serbia)

Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.

Floods enhance the abundance and diversity of anthropogenic microparticles (including microplastics and treated cellulose) transported through karst systems

Microplastics (plastics <5 mm) are emerging contaminants that have been detected in virtually all environments. While microplastic research in terrestrial surface waters has been proliferating, microplastic contamination in subsurface environments remains understudied. Karst terrains may be particularly susceptible to microplastic pollution because the presence of large dissolution openings allows fast transport of water through these systems, facilitating the introduction of surface contaminants into subsurface habitats. Furthermore, few studies address the prevalence and movement of microparticles composed of semisynthetic and modified natural materials, despite their known ecotoxicity. Our study therefore aims to identify anthropogenic (i.e., synthetic, semisynthetic, and treated natural) microparticle extent, sourcing, and transport in subsurface karst environments. To do so, we examined a cave spring under variable flow conditions, finding that anthropogenic microparticles were present in all samples and were most frequently fibrous and clear. The mean anthropogenic microparticle concentration during baseflow was 9.2 counts/L but increased up to 81.3 counts/L during floods, indicating their enhanced mobilization when relatively dilute, acidic, and sediment-rich event water entered the cave. These results suggest that anthropogenic microparticles may originate from surface recharge or sediment resuspension within the cave. When we analyzed a subset of microparticles with Fourier transform infrared spectroscopy (FTIR), we found that cellulose of known (i.e., dyed) and suspected (i.e., clear) anthropogenic origin was the most abundant material type. We nevertheless confirmed the presence of microplastics in the cave stream under all flow conditions, with the most common polymer being polyethylene. Both the concentrations and relative fractions of microplastics were higher during floods compared to baseflow, indicating their increased transport during high flow events. We also observed that microplastic polymer types diversified as discharge increased. Our study gives new insight into how anthropogenic microparticle contamination is transported through karst landscapes that can help inform debris mitigation strategies to protect ecosystems and water resources.

Evolutionary modifications of Astyanax larval prey capture (LPC) in a dark environment

Feeding strategies of an organism depend on the multimodal sensory processing that most efficiently integrates available visual, chemosensory, and/or mechanoreceptive cues as part of their environmental adaptation. The blind cavefish morph of Astyanax mexicanus has developed sensory-dependent behaviors to find food more efficiently than their eyed, surface-morph counterparts while in darkness. In the absence of light, adult cavefish have evolved enhanced behaviors, such as vibration attraction behavior (VAB), and changes in feeding angle. Here, we identified evolved differences in cavefish larval prey capture (LPC) behavior. In the dark, LPC is more efficient in cavefish than in surface fish. Furthermore, different cave populations express laterality in their LPC and strike towards prey preferentially located on their left or right sides. This suggests the occurrence, to some extent, of divergent LPC evolution among cave populations. While LPC can be triggered exclusively by a vibration stimulus in both surface and cavefish, we provide evidence that LPC is, at least partially, a multimodal sensory process different from adult VAB. We also found that a lack of food may exacerbate the laterality of LPC. Thus, we proposed a mathematical model for explaining laterality based on a balance between: (1) enlarged range of foraging field (behavioral or perceptive) due to asymmetry, (2) food abundance, and (3) disadvantages caused by laterality (unequal lateral hydrodynamic resistance when swimming, allocation of resources for the brain and receptors, and predator escape).

Evaluation of water and sediment quality of İnaltı Cave (Northern Türkiye) by using multivariate statistical methods

Heavy metals, which are among the important pollutants that threaten ecosystems, have been a particularly intriguing subject of accumulation studies. The present study aimed to reveal the water and sediment quality, pollution status, and their usability for living organisms in 10 stations for the first time in İnaltı cave, which has two underground ponds. Concentrations of 9 heavy metals (Cu, Pb, Zn, Ni, Mn, Fe, Cd, Cr, Al) and 1 metalloid (As) were determined in samples taken. These results were compared to the limit values in Sediment Quality Guides (SQGs) and analyzed further using different sediment evaluation methods. SQG values revealed that the amounts of Cd and Ni are of concern. Examining the concentrations of metals in the water, the ranking by concentration was found to be Al > Cr > Pb > Cu > As > Mn and the elements were considered not to pose any environmental risk. The enrichment of detected Cd metal in the sediment is remarkable. In addition, ANOVA, Pearson's correlation analysis, principal component analysis (PCA), and hierarchical clustering analysis were carried out in order to make the obtained data easier to understand and interpret. While designing the most appropriate action plans for water management, more clear and understandable information can be obtained by using these methods and interpreting the raw data. In the cave, individuals belonging to the Niphargus genus, a member of the Malacostraca class, Niphargidae Family, were identified in the sediment.

Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution

BACKGROUND

Transcriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species' ability to interbreed and generate hybrid individuals.

RESULTS

We generated transcriptomes of the Rakov Škocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F₁ hybrids between cave and surface individuals. RNAseq of F₂ hybrids, as well as genotyping of a backcross, allowed for positional information of multiple candidate genes from the differential expression and allele-specific analyses.

CONCLUSIONS

As expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F₁ hybrids identified genes with cave-biased (cave allele has higher mRNA levels than the surface allele) and surface-biased expression (surface allele has higher mRNA levels than the cave allele). RNAseq of F₂ hybrids allowed for multiple genes to be placed to previously mapped genomic regions responsible for eye and pigmentation phenotypes. In the future, these transcriptomic resources will guide prioritization of candidates for functional analysis.

Growth stage-related biomass, pigments, and biochemical composition of Stichococcus bacillaris, Synechococcus sp., and Trentepohlia aurea isolated from Gua Tempurung, a cave in Malaysia

As part of the lampenflora that inhabit limestone caves, microalgae play an important role in cave ecosystems but are understudied in tropical ecoregions. In the present study, the dominant eukaryotic and prokaryotic microalgae identified in lampenflora samples collected from Gua Tempurung, a cave in Malaysia, and growth stage-related microalgal attributes were determined. Stichococcus bacillaris, Synechococcus sp., and Trentepohlia aurea were selected and cultured in Bold's Basal Medium (S. bacillaris and T. aurea) or BG-11 medium (Synechococcus sp.) under laboratory conditions. The highest specific growth rate (0.72 ± 0.21 day^-1) and dry weight (0.11 ± 0.04 mg L^-1) were recorded in S. bacillaris in the early stationary phase. Trentepohlia aurea and Synechococcus sp. had the highest ash-free dry weight and total ash percentage (11.18 ± 4.64 mg L^-1 and 8.55% ± 6.73%, respectively) in the early stationary phase. Stichococcus bacillaris had the highest moisture content (84.26% ± 0.64%) in the exponential phase. Chlorophylls a and b were highest in the early stationary phase in T. aurea (0.706 ± 0.40 mg L^-1 and 1.094 ± 0.589 mg L^-1, respectively). Carotenoid levels were highest in Synechococcus sp. in the early stationary stage (0.07 ± 0.02 mg L^-1). Lipids were the major biochemical compound identified at the highest levels in Synechococcus sp. (67.87% ± 7.75%) in the early stationary phase, followed by protein recorded at the highest levels in T. aurea (57.99% ± 4.99%) in the early stationary phase. Carbohydrates were the compound identified least often with the highest recorded levels found in T. aurea (9.94% ± 0.49%) in the late stationary phase. Biomass, pigments, and biochemical accumulation varied at different growth stages in the studied microalgae, and this variation was species-specific. The present study provides a benchmark for the growth phases of aerophytic cave microalgae, which will be useful for determining their optimum harvest time and obtaining biochemical compounds of interest.

Review of studies about bat-fly interactions inside roosts, with observations on partnership patterns for publications

Pressures from anthropogenic disturbances have triggered a wealth of studies focusing on the assessment and mitigation of the negative impacts of these disturbances on inter and intraspecific ecological interactions, including bats and bat flies in their roosts. The heterogeneity of research methods employed for these studies and the scientific imbalance between countries may constrain advances and the consolidation of the knowledge on this subject. We reviewed the literature regarding bat and bat-ectoparasite interactions in roosts assessing global research trends and patterns of author collaborative work to be able to identify key questions for future studies and potential initiatives to improve the knowledge on this subject. Current information available has mostly come from the Americas and is predominantly focused on the recognition and description of parasite-host interactions between bats and bat flies. Our findings suggest the value of increasing collaboration for future research, as several countries with largely diverse environments and high organismal richness are disconnected from the countries that produce the most publications in this area, and/or have low records of publications. These regions are in the Global South, mostly in South American and African countries. We suggest that more collaborative networks may increase scientific production in the area, and that investing in local research development and enhancing partnerships for publications may strengthen the field. These research programs and collaborations are key for the development of conservation strategies for bats and bat flies, for their roosts, and for understanding bat and bat-ectoparasite interactions.

Revision of the javanicus species group of the millipede genus Glyphiulus Gervais, 1847, with descriptions of five new species from China (Diplopoda, Spirostreptida, Cambalopsidae)

The javanicus-group of Glyphiulus is re-assessed and its Chinese component species are presently divided between the following two newly-circumscribed species groups, i.e. the formosus- and the sinensis-group. The two can be differentiated, based on the diagnostic characters of the first pair of legs in the male. In addition, metatergal crests being complete and the carinotaxy formula on the collum being I-III+P+M are only characteristic of the formosus-group. A molecular phylogeny of the genus, based on DNA sequencing of four gene fragments of four genes, allows for Glyphiulus to be recovered as a monophyletic group, the phylogenetic relationship being ((Clade A, Clade B), Clade C). Molecular evidence is fully congruent with the morphological one. In addition, based on barcoding data, interspecific p-distances between Glyphiulus species amount to 11.2-24.9%, vs. 0-8.2% for intraspecific p-distances. Five new species of Glyphiulus, all cavernicolous, are described from China: G.sinuatoprocessus Zhao & Liu, sp. nov., G.conuliformis Zhao & Liu, sp. nov. (both from Guangdong Province), G.xiniudong Zhao & Liu, sp. nov., G.scutatus Zhao & Liu, sp. nov. and G.portaliformis Zhao & Liu, sp. nov. (all three from Guangxi Zhuang Autonomous Region). The known Chinese species of the formosus-group appear to mainly be confined to the South China region.

eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects

Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.

Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov

An actinobacterial strain, designated YC3-6^T, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10-30 °C, pH 5.0-10.0 and 0-4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family Nocardiaceae. Levels of 16S rRNA gene similarity indicated that the close relatives are Rhodococcus cavernicola (98.4% sequence similarity) and "Rhodococcus psychrotolerans" (98.2%) followed by Antrihabitans stalactiti (96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with A. stalactiti and was separated from R. cavernicola and other members of the family Nocardiaceae. The morphological and chemotaxonomic characteristics of strain YC3-6^T are in line with those of the genus Antrihabitans. Strain YC3-6^T showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with A. stalactiti. In addition, the core gene analysis showed that R. cavernicola formed a distinct subline between an Antrihabitans cluster and Aldersonia kunmingensis, and well separated from members of the genus Rhodococcus. The average amino acid identity values of R. cavernicola to closely related neighbours were 69.3-69.4% with members of the genus Antrihabitans and 67.3% with Ald. kunmingensis, while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6^T is concluded to represent a novel species of the genus Antrihabitans, for which the name Antrihabitans stalagmiti sp. nov. (type strain, YC3-6^T = KACC 19963^T = DSM 107561^T) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that R. cavernicola Lee et al. 2020 be transferred to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov., comb. nov.

Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo

Objective

Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed.

Results

CoV-RNA was detected in ten specimens (47.6%, n  = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.

Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species

We present a molecular phylogenetic analysis including a survey for overlooked phenotypic characters. Based on both analysis and characters a new cave-dwelling species is described: Tityus (Tityus) spelaeussp. nov. from the Russão II cave, Posse, state of Goiás, Central Brazil. Characters such as the glandular regions of the female pectinal basal piece and basal middle lamellae of pectines, and the distribution of the ventral setae of telotarsi I-IV proved to be useful to constructing the taxonomy of species and species groups of Tityus. The new species is a member of the Tityustrivittatus species-group of Tityus (Tityus) and can be readily recognized by the immaculate coloration pattern and the more developed glandular region on the female pectinal basal piece. In addition, we provide a discussion of the phylogenetic relationships observed within Tityus, on the relevance of the new phenotypic characters to the modern taxonomy of the genus Tityus, and to the records of Brazilian cave scorpions.

Two new species of the millipede genus Glyphiulus Gervais, 1847 (Diplopoda, Spirostreptida, Cambalopsidae) from caves in northern Thailand

Two new species of the genus Glyphiulus Gervais, 1847 are described and illustrated. The first species, G.longus sp. nov., is the second species of the javanicus-group to be found in Thailand. It resembles G.guangnanensis Jiang, Guo, Chen & Xie, 2018, from southern China, but is distinguished by a smaller size and the carinotaxic formula of the collum, combined with ♂ legs 1 bearing very strongly reduced telopodites, the anterior gonopods showing a pair of very long and slender apicomesal processes, and the denser plumose and stout flagella of the posterior gonopods. The second species, G.promdami sp. nov., the fifth member of the granulatus-group in Thailand, seems to be particularly similar to G.subbedosae Likhitrakarn, Golovatch & Panha, 2017, from Laos. However, it can be distinguished from the latter species mainly by showing a uniformly yellow collum and the posterior gonopod coxite bearing several strong setae in median and lateral views, coupled with the anterior gonopod coxosternum being microsetose in the anterior and medial parts in caudal view. An identification key to, and a distribution map of, all seven Glyphiulus species currently known to occur in Thailand are also provided.

Arcellinida testate amoebae as climate miner's canaries in Southern Spain

Southern Spain is currently under threat of desertification as a consequence of global climate change, which pressures on fragile ecosystems such as caves. The organisms living in these extremely stable environments are particularly sensitive and prone to extinction, therefore they can be used as bioindicators for climate change. Cyanobacterial mats form peculiar and vulnerable micro-ecosystems at the entrance of caves and house a diversity of protists. Amongst them, Arcellinida testate amoebae have been traditionally used as bioindicators for environmental quality, notably because their narrow ecological tolerance and their key ecological position as top predators of the microbial foodwebs. We report here two new species of Arcellinida found in the cyanobacterial mats of cave Hundidero, in Sierra de Grazalema, Malaga province, whose traits suggest a narrow tolerance for changes in humidity. We provide a formal description for Difflugia alhadiqa sp. nov. and Heleopera baetica sp. nov. based on morphometrics and 18S rRNA gene data, and propose using the presence of these species to indicate the good health of the cyanobacterial mats, like miner's canaries for local climate.

Understanding the linkage between regional climatology and cave geochemical parameters to calibrate speleothem proxies in Madagascar

Robust reconstructions of paleoclimate and paleoenvironmental changes using stalagmite proxy records critically depend on detailed observations of the transfer function between the regional climate/environment, the karst aquifer hydrology, and finally the cave microclimate via monitoring, which is currently lacking in Madagascar. This paper reports the first monitoring study performed in Anjohibe Cave, in Mahajanga, NW Madagascar to understand the linkage between regional climatological changes and cave responses to such changes. In this research, we monitored (1) the drip water pH, TDS, EC, temperature, δ¹³C_DIC, δ¹⁸O_w, δ²H_w, and elemental (Ca, Mg, Sr) composition, and (2) the cave atmosphere pCO₂, relative humidity (RH) and temperature. Three significant findings were drawn from the results. First, the data show that air-to-air transfer is fast, and the internal parameters closely vary with the regional climatology. Second, rainfall to drip signal transfer is not immediate, and it can take few months to one season for the signals to be detected in the drip water due to the "epikarst storage effect". Lastly, CaCO₃ precipitation is likely to occur during the winter-summer transition, during which prior carbonate precipitation was detected. Since the growth of speleothems is influenced by numerous cave-specific factors, this study, although preliminary, indicates that Anjohibe Cave drip waters are capable of registering changes in its surrounding environment. Such information is ultimately archived in speleothems to reconstruct paleoclimate and paleoenvironmental changes. Results from this research will be of high significance for those working on speleothems within Madagascar, and for those working on understanding the transfer of climatic variations to cave deposits.

Composition of nutrient media and temperature of cultivation imposes effect on the content of secondary metabolites of Nocardiopsis sp. isolated from a Siberian Cave

Growth of human population leads to many global and medical problems. The problems include the crisis of health, antibiotic resistance, drug discovery, etc. Increasing antimicrobial resistance of microorganisms results in the need to screen natural products (incl. antibiotics and antimicrobial peptides) and their producers in different ecological niches. The purpose of this study was to estimate antibiotic activity and biotechnological potential of rare actinobacteria Nocardiopsis sp. The strain was isolated from Okhotnichya cave located in Siberia. Here, we cultivated the strain at 3 temperature modes (13 °C, 28 °C, 37 °C) in 11 liquid nutrient (rich and poor) media. Using modern assays of liquid chromatography and high-resolution mass spectrometry, we estimated the content and number of produced natural products, distribution of their masses, and potential rate of novel secondary metabolites. We demonstrated that minimal nutrient media with l-asparagine and SM25 media with malt extract were less productive at current experimental parameters. As it was shown, this strain was characterized by antibiotic properties against Bacillus subtilis when cultivated at 28 °C. Also, weak antibiotic activity of crude extracts was found in strain cultivation at 13 °C. Also, we detected a high number of novel amphiphilic and hydrophobic NPs produced by this strain. We demonstrated both the influence of the nutrient media composition and cultivation temperature on biosynthetic capabilities of rare strain Nocardiopsis sp. Finally, high level of natural products that were predicted as novel confirms high biotechnological value of rare genera of Actinobacteria that could be explained by the evolution of microorganisms in the isolated environment of cave ecosystem.

Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology

Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats.

Environment-driven control of fungi in subterranean ecosystems: the case of La Garma Cave (northern Spain)

Airborne microorganisms can cause important conservation problems in caves with Paleolithic art and therefore the knowledge of cave aerodynamic is essential. La Garma Cave (Cantabria, Spain), an exceptional archaeological site with several levels of galleries interconnected and two entrances, presents a complex atmospheric dynamics. An approach including aerobiological sampling together with microclimate monitoring was applied to assess the factors controlling the origin of airborne fungi. Here we show that winter ventilation is critical for the increasing of Basidiomycota spores in the cave air and the highest concentrations were found in the most ventilated areas. On the contrary, Ascomycota spores prevailed in absence of ventilation. Besides, most Ascomycota were linked to insects and bats that visit or inhabit the cave. The combination of aerobiological and microclimate data constitutes a good approach to evaluate the influence of external climatic conditions and design the most suitable strategies for the conservation of cultural heritage in the cave environment.

Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)

Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.

Factors inducing bryophyte growth on prehistoric pigments and effect of UV-C treatment

In La Glacière cave (France), the touristic activity has been conducted to an environmental parameter change that has led to photosynthetic organism proliferation (microalgae, diatoms, cyanobacteria, bryophytes). The present study is focused on bryophyte development occurring in the show cave that was responsible of limestone biodeterioration. In order to understand the colonization process of limestone, we have maintained limestone blocks under optimal Lampenflora growth conditions. Moreover, some limestone blocks were painted with several pigments that were used in the prehistory (e.g., red ocher, bone char). Microorganisms and bryophyte growth were monitored during 1 year, and then, the block samples were treated using UV-C light (254 nm). Thus, obtained results were compared with in situ treatment in La Glacière cave. Results have showed dense bryophyte propagation on the several blocks. However, the growth rate was correlated with the chemical composition of the pigment. In fact, the presence of some chemical elements such as As, Cr, Ti, and Co contributed to reduce bryophyte growth. Finally, moss treatment using UV-C light has demonstrated high efficiency under in situ condition, while a fast recolonization has been observed for samples maintained in laboratory. This difference was explained by the high bryophyte density under laboratory conditions that make UV-C light penetration difficult.

Ecology of Antricola ticks in a bat cave in north-eastern Brazil

Argasid ticks are a diverse group of acarines that parasitize numerous vertebrate hosts. Along with birds, bats serve as hosts for several argasid ticks, which are commonly found in bat caves. Argasid ticks have regained attention from tick taxonomists in recent decades, with a number of new species described in various zoogeographical regions. Nonetheless, studies on their ecology are still scarce. We conducted a 1-year longitudinal study to assess the presence of argasid ticks in a bat cave in the drylands of north-eastern Brazil and evaluate their possible response to abiotic factors. From July 2014 to June 2015, 490 ticks were collected (272 nymphs, 169 males and 49 females) in a cave chamber hosting a large colony of Pteronotus spp. bats, being relatively more frequent from July to December 2014. Adults were identified as Antricola guglielmonei, whereas nymphs were assigned to the genus Antricola. Almost all ticks (98%) were collected on the cave walls. Only 2% were on the ceiling and, surprisingly, no specimens were found on the floor and/or guano. Adults were usually clustered in the crevices and little mobile, whereas nymphs were dispersed and more active, moving over the walls or ceiling of the cave. Although present in most of the studied period, there was a significantly negative correlation between tick abundance and relatively humidity, and A. guglielmonei was more frequent during the dry season. Moreover, there was no evident correlation between the abundance of ticks and bats. Further long-term studies will be able to verify whether this pattern is repeated over time, and even whether other variables can influence the population dynamics of A. guglielmonei.

Phlebotomine (Diptera: Psychodidae) fauna in a cavern containing cave paintings and its surrounding environment, Central-West Brazil

The interior of caves usually presents climate, light, soil, flora and fauna that distinguish it from the external environment. Among the sandfly species found in caves, several may act as vectors of Leishmania spp. and others are a nuisance to humans due to their painful bites. This study sought to identify the phlebotomine fauna in a cavern with cave paintings ("Gruta do Pitoco") which attract tourists in Alcinopólis municipality, Mato Grosso do Sul state, Brazil. The sandflies were collected from March 2014 to September 2015, with automatic light traps, installed monthly, in the entrance and interior of the cave and outside it. A total of 7645 specimens belonging to 27 species were collected. Lutzomyia dispar, Martinsmyia oliverai and those of the Lu. longipalpis complex (Lu. cruzi and Lu. longipalpis) were the predominant species. Among the three environments sampled, no great difference between species richness was observed. Comparing these environments, the interior of the cave presented the lowest diversity index due to the high frequency of Lu. dispar (46%). For the first time, specimens (only females) of the genus Deanemyia were collected in Mato Grosso do Sul state. Moreover, the study revealed the sympatric occurrence of Lu. cruzi and Lu. longipalpis, both proven vectors of L. infantum, and also Lu. dispar, a highly anthropophilic species, which often causes annoyance to those who visit the cave.

An unusual case of bovine anthrax in the canton of Jura, Switzerland in 2017

Background

Anthrax caused by Bacillus anthracis is a zoonotic disease mainly affecting herbivores. The last Swiss outbreak was over 20 years ago. We describe a recent anthrax outbreak involving two cows from the same herd. One cow was designated as a peracute clinical case with sudden death and typical lung lesions, while the other cow presented with protracted fever and abortion.

Case presentation

On April 29th 2017, a 3.5-year-old Montbéliard dairy cow was found dead while out at pasture with haemorrhage from the nose. The veterinarian suspected pneumonia and performed a necropsy on site. Subsequently, a lung and liver sample were sent to the laboratory. Unexpectedly, Bacillus anthracis was isolated, a pathogen not found in Switzerland for decades. Several days later, a second cow from the same farm showed signs of abortion after protracted fever. Since these symptoms are not typical for anthrax, and the bacteria could not be demonstrated in blood samples from this animal, a necropsy was performed under appropriate biosafety measures. Subsequently, Bacillus anthracis could be isolated from the placenta and the sublumbal lymph nodes but not from the blood, liver, spleen and kidney. The outbreak strain (17OD930) was shown to belong to the lineage B.Br.CNEVA, the same as Swiss strains from previous outbreaks in the region. We speculate that the disease came from a temporarily opened cave system that is connected to an old carcass burial site and was flushed by heavy rainfall preceding the outbreak.

Conclusion

Even in countries like Switzerland, where anthrax is very rare, new cases can occur after unusual weather conditions or ground disturbance. It is important for public officials to be aware of this risk to avoid possible spread.

On the genera Qiongocera and Relictocera (Araneae, Psilodercidae) from Southeast Asia

Four new species are described in two psilodercid genera, Qiongocera Li & Li, 2017 and Relictocera Li & Li, 2017: Qiongoceraluoxuan Li & Li, sp. nov. (♂♀) from China, Relictocerawugen Li & Li, sp. nov. (♂♀) and R.sigen Li & Li, sp. nov. (♂) from Vietnam, and R.qianzi Li & Li, sp. nov. (♂♀) from Thailand. These genera were previously thought to be monotypic. In addition, one species of the genus Merizocera Fage, 1912 is transferred to Relictocera: Relictoceramus (Deeleman-Reinhold, 1995), comb. nov. (♂♀). The types of the new species are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing.

Description of the male and the larva of Ixodes collaris Hornok, 2016 with drawings of all stages

Background

Ixodes collaris Hornok, 2016 is a recently discovered tick species associated with bats in Asia. This study provides the description of the male and the larva, as well as high quality drawings of all stages.

Methods

Ticks were collected from cave walls and bats in Phia Oac (Vietnam). DNA was extracted from one individual of each stage/sex, while another was morphometrically analysed. Based on two genetic markers, all ticks were identified as I. collaris.

Results

The male of I. collaris has long legs (i.e. the length of Haller’s organ exceeds the maximum diameter of tarsus I), unlike the male of I. simplex Neumann, 1906, but similarly to males of I. vespertilionis Koch, 1844 and I. ariadnae Hornok, 2014. The lateral and medial edges of the palpi of male I. collaris are both convexly curved, unlike in I. ariadnae and I. simplex, but similarly to I. vespertilionis. The male of I. collaris has long palpal setae (up to 210 µm), unlike the males of I. ariadnae (30–100 µm) and I. simplex (20–80 µm), but similarly to I. vespertilionis (100–200 µm). Males of I. collaris have sparse distribution of long palpal setae (vs dense in I. vespertilionis) and posteriorly diverging, sclerotized trapezoid ridge dorsally on the basis capituli (posteriorly convergent, U-shaped and less evident in I. vespertilionis). The larva of I. collaris has long legs (unlike the larva of I. simplex, but similarly to I. vespertilionis and I. ariadnae), elongated club-shaped palpi (240 × 70 vs 200 × 90 µm in I. ariadnae, 200 × 70 µm in I. vespertilionis; and 140 × 60 µm in I. simplex:), pentagonal scutum, which is longer than broad (different from I. ariadnae and I. simplex, but similar to that of I. vespertilionis). The larva of I. collaris has strongly concave caudolateral margin of ventral basis with perpendicular angle (vs slightly concave, with obtuse angle in I. vespertilionis) and a prominent, dark sclerotized edge, “collar” (absent in I. vespertilionis).

Conclusion

Several features allow to distinguish the male and the larva of I. collaris morphologically from those of other bat-associated ixodid tick species.

A Study on actinobacterial diversity of Hampoeil cave and screening of their biological activities

Caves are oligotrophic, dark and less-explored environments and are considered as sources of promising microbial strains in biotechnology. Hampoeil Cave is located in massive dolomite with thin bedded limestone in northwestern of Iran. In an isolation and screening program, various samples from soil, water, floor, wall and ceiling of Hampoeil cave and its invertebrates were collected. Four various treatments and 10 different isolation media were used for the isolation of the actinobacteria. Screening of the isolates for antimicrobial activity against 10 bacteria and fungi, 5 hydrolytic enzymes production and resistance to 5 heavy metals have been performed. Among 33 various samples, 76 actinobacteria from various genera, including Streptomyces, Micromonospora, Micrococcus, Kocuria and Corynebacterium were isolated. Eighty percent of the strains had one of the studied hydrolytic enzyme activity. At least one type of antimicrobial activity was seen in 25.3% of the isolates. Resistance to one metal or more was seen in 26.32% of the isolates. The ratio of rare-actinobacteria in the oligotrophic samples to enriched samples is 20% more than Streptomyces. Percentage of strains with the highest activity in esterase, amylase, DNase, protease or lipase activity that were isolated from organic-rich environmental samples were 100, 100, 100, 82 and 82%, respectively. Also, 26.32% of the actinobacterial isolates resisted to heavy metals. It was concluded that Hampoeil cave is a good source in finding cave-living actinobacteria potent in producing hydrolytic enzymes and bioremediation.

Diversity Of Mosquito Species Ovipositing In Different Zones of Light Intensity Within Limestone Caves In Thailand

Climate change and human activity affect the geographical and annual distribution and population abundance of mosquitoes. As natural habitats are reduced, it is hypothesized that mosquitoes may seek refuge in more stable environments such as cave habitats. Therefore, we explored the species diversity of mosquitoes exploiting cave habitats in Thailand. Ten species belonging to 4 genera were collected, of which none were considered to be true cave-dwelling species (Troglobiont). The known cavernicolous species, Aedes cavaticus, was observed to oviposit outside of the cave and therefore should be categorized as a subtroglophilic species. Other species were also oviposited inside the cave but should be regarded as trogloxenic species. There was no clear association between environmental factors and mosquito abundance inside the 4 limestone caves, except for Ae. cavaticus, which was positively correlated with rainfall. This study indicates that different biotic or abiotic factors may be involved in mosquito oviposition site selection inside caves.

Multiple transgressions and slow evolution shape the phylogeographic pattern of the blind cave-dwelling shrimp Typhlocaris

Background

Aquatic subterranean species often exhibit disjunct distributions, with high level of endemism and small range, shaped by vicariance, limited dispersal, and evolutionary rates. We studied the disjunct biogeographic patterns of an endangered blind cave shrimp, Typhlocaris, and identified the geological and evolutionary processes that have shaped its divergence pattern.

Methods

We collected Typlocaris specimens of three species (T. galilea, T. ayyaloni, and T. salentina), originating from subterranean groundwater caves by the Mediterranean Sea, and used three mitochondrial genes (12S, 16S, cytochrome oxygnese subunit 1 (COI)) and four nuclear genes (18S, 28S, internal transcribed spacer, Histon 3) to infer their phylogenetic relationships. Using the radiometric dating of a geological formation (Bira) as a calibration node, we estimated the divergence times of the Typhlocaris species and the molecular evolution rates.

Results

The multi-locus ML/Bayesian trees of the concatenated seven gene sequences showed that T. salentina (Italy) and T. ayyaloni (Israel) are sister species, both sister to T. galilea (Israel). The divergence time of T. ayyaloni and T. salentina from T. galilea was 7.0 Ma based on Bira calibration. The divergence time of T. ayyaloni from T. salentina was 5.7 (4.4-6.9) Ma according to COI, and 5.8 (3.5-7.2) Ma according to 16S. The computed interspecific evolutionary rates were 0.0077 substitutions/Myr for COI, and 0.0046 substitutions/Myr for 16S.

Discussion

Two consecutive vicariant events have shaped the phylogeographic patterns of Typhlocaris species. First, T. galilea was tectonically isolated from its siblings in the Mediterranean Sea by the arching uplift of the central mountain range of Israel ca. seven Ma. Secondly, T. ayyaloni and T. salentina were stranded and separated by a marine transgression ca. six Ma, occurring just before the Messinian Salinity Crisis. Our estimated molecular evolution rates were in one order of magnitude lower than the rates of closely related crustaceans, as well as of other stygobiont species. We suggest that this slow evolution reflects the ecological conditions prevailing in the highly isolated subterranean water bodies inhabited by Typhlocaris.

Penicillium gravinicasei, a new species isolated from cave cheese in Apulia, Italy

Several species of the genus Penicillium were isolated during a survey of the mycobiota of Apulian cave cheeses ripened in a cave in Gravina di Puglia, Italy. A novel species, Penicillium gravinicasei, is described in Penicillium section Cinnamopurpurea. Its taxonomic novelty was determined using a polyphasic approach, combining phenotypic, molecular (β-tubulin, calmodulin, ITS and DNA dependent RNA polymerase) DNA sequences and mycotoxin production data. Phylogenetic analyses of the RPB2 data showed that isolates of the novel species form a clade most closely related to Penicillium cinnamopurpureum and P. parvulum with high bootstrap support. The fungus did not produce ochratoxin A, citrinin, patulin, sterigmatocystin or aflatoxin B₁ on standard agar media. The novel species had a high growth rate on agar media supplemented with 5% NaCl, and could be distinguished from other Penicillium section Cinnamopurpurea species by phenotypic and molecular characteristics.

Continuous monitoring of radon gas as a tool to understand air dynamics in the cave of Altamira (Cantabria, Spain)

The use of radon as an atmospheric tracer in the Altamira Cave over the past 30years has provided relevant information about gaseous exchanges between the Polychromes Room, the adjoining Chambers inside the cave, and the outside atmosphere. The relatively simple physico-chemical behaviour of radon gas provides a marked advantage over other tracer gases that are usually present in high concentrations in hypogeous environments, such as CO₂. Two types of continuous radon measurement were undertaken. The first involves active detectors located in the Hall and Polychromes Room, which provide radon concentration values at 1-hour intervals. In addition, nuclear solid track etched detectors (CR-39) are used in every chamber of the cave over 14-day exposure periods, providing average radon concentrations. In this paper we show some of the specific degassing and recharge events identified by anomalous variations in the concentration of radon gas in the Polychromes Room. In addition, we update knowledge regarding the degree of connection between chambers inside the cave and with the outside atmosphere. We verify that the connection between the Polychromes Room and the rest of the cave has been drastically reduced by the installation of the second closure in 2008. Except for point exchanges with the Crossing zone generated by a negative temperature gradient in that direction, the atmosphere of the Polychromes Room remains stable, or else it exchanges matter with the outside atmosphere through the karst interface. The role of radon as a tracer is demonstrated to be valid both to reflect seasonal cycles of degassing and recharge, and to analyse shorter (daily) period fluctuations.

Seven new freshwater species of Gammarus from southern China (Crustacea, Amphipoda, Gammaridae)

Seven new species of the genus Gammarus are described and illustrated from southern China. The new species Gammarus vallecula Hou & Li, sp. n., G. qinling Hou & Li, sp. n., G. zhigangi Hou & Li, sp. n. and G. jidutanxian Hou & Li, sp. n. are characterized by inner ramus of uropod III half the length of outer ramus. Gammarus longdong Hou & Li, sp. n. is characterized by inner ramus of uropod III 0.9 times as long as outer ramus. Gammarus mosuo Hou & Li, sp. n. is characterized by pereopods V-VII with long setae on anterior margins and both rami of uropod III armed with simple setae. Gammarus caecigenus Hou & Li, sp. n. can be distinguished from other species by eyes absent. DNA barcodes of the new species are documented as proof of molecular differences between species. A key to the new species and a map of their distributions are provided.

Four new species of the Glyphiulus javanicus group from southern China (Diplopoda, Spirostreptida, Cambalopsidae)

Hitherto, 24 species of the Glyphiulusjavanicus group have been recorded, all endemic to Southeast Asia, including 14 in China. Nevertheless, this species group needs further exploration. In this context, four new species of this group are described, all collected from limestone caves in Southern China: G.calceussp. n., G.foetidussp. n., G.guangnanensissp. n., and G.impletussp. n. They can be separated easily from each other and other congeners by their carinotaxic formulae, the structures of male legs I, and the gonopods. Due to the absence of any troglomorphic traits in our specimens, they may be troglophilic only.

Batracobdella leeches, environmental features and Hydromantes salamanders

Leeches can parasitize many vertebrate taxa. In amphibians, leech parasitism often has potential detrimental effects including population decline. Most of studies on the host-parasite interactions involving leeches and amphibians focus on freshwater environments, while they are very scarce for terrestrial amphibians. In this work, we studied the relationship between the leech Batracobdella algira and the European terrestrial salamanders of the genus Hydromantes, identifying environmental features related to the presence of the leeches and their possible effects on the hosts. We performed observation throughout Sardinia (Italy), covering the distribution area of all Hydromantes species endemic to this island. From September 2015 to May 2017, we conducted >150 surveys in 26 underground environments, collecting data on 2629 salamanders and 131 leeches. Water hardness was the only environmental feature correlated with the presence of B. algira, linking this leech to active karstic systems. Leeches were more frequently parasitizing salamanders with large body size. Body Condition Index was not significantly different between parasitized and non-parasitized salamanders. Our study shows the importance of abiotic environmental features for host-parasite interactions, and poses new questions on complex interspecific interactions between this ectoparasite and amphibians.

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Sardinian Hydromantes salamanders are often parasitized by Batracobdella algira.

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Underground presence of B. algira is strongly associated to active karstic systems.

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Leeches often parasitize large-sized salamanders.

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Parasitism of B. algira does not affect Body Condition Index of salamanders.

Two new species of the millipede genus Glyphiulus Gervais, 1847 from Laos (Diplopoda, Spirostreptida, Cambalopsidae)

Two new species of Glyphiulus are described and illustrated from northern Laos. The epigean Glyphiulussubbedosae Likhitrakarn, Golovatch & Panha, sp. n. is the second member of the granulatus-group to be found in that country and it seems to be especially similar to G.bedosae Golovatch, Geoffroy, Mauriès & VandenSpiegel, 2007. However, it differs from the latter species by a row of several strong setae near the median marginal ridge on the paraprocts, combined with the gnathochilarium being considerably less densely setose on the caudal face, and the anterior gonopods showing a pair of smaller, apical, but larger lateral teeth on the coxosternal plate. Glyphiulussemicostulifer Likhitrakarn, Golovatch & Panha, sp. n. is the fourth member of the javanicus-group to be discovered in Laos, taken from a cave. It seems to be particularly similar to G.costulifer Golovatch, Geoffroy, Mauriès & VandenSpiegel, 2007, but is distinguished by the more sparsely alveolate background fine structure of the metazonae, coupled with the gnathochilarium being considerably less densely setose on the caudal face, much stronger paramedian prongs and 4-segmented telopodites on ♂ coxae 1, the slightly longer and more slender apicoparamedian sternal projections on the anterior gonopods, and the much longer flagella of the posterior gonopods. An identification key to and a distribution map of Glyphiulus species in Laos are also presented.

Comparing growth in surface and cave morphs of the species Astyanax mexicanus: insights from scales

Background

Life in the darkness of caves is accompanied, throughout phyla, by striking phenotypic changes including the loss or severe reduction in eyes and pigmentation. On the other hand, cave animals have undergone constructive changes, thought to be adaptive, to survive in this extreme environment. The present study addresses the question of the evolution of growth in caves, taking advantage of the comparison between the river-dwelling and the cave-dwelling morphs of the Mexican tetra, Astyanax mexicanus.

Results

A sclerochronology approach was undertaken to document the growth of the species in these two very distinct habitats. Scales from 158 wild Astyanax mexicanus specimens were analyzed from three caves (Pachón, Tinaja and Subterráneo) and two rivers (Rio Gallinas and Arroyo Lagarto) in San Luis Potosi and Tamaulipas, Mexico. A 10–13% reduction in scales size was observed in the cave morphs compared to the surface morphs. Age could be reliably inferred from annual growth increments on the scales from the two morphs of the species. Further comparisons with growth curves in laboratory conditions, obtained using the von Bertalanffy growth model, were also performed. In the wild and in the laboratory, cavefish originating from the Pachón cave reached smaller sizes than surface fish from three different locations: Rio Gallinas and Arroyo Lagarto (wild sampling) and Texas (laboratory population), respectively. Wild Pachón cavefish also seemed to grow to smaller sizes than the two other wild cavefish populations studied, Tinaja and Subterráneo. Finally, growth in the laboratory was faster than in the wild, particularly in the two first years of life.

Conclusions

These data suggest that cavefish originating from the Pachón cave are subjected to an intrinsic limitation of their final size, which is at least in part independent from energy/food availability. This growth limitation may be an advantageous way of limiting energy expenditure and food needs in the cave environment. Moreover, growth regulation evolved differently in independently evolved cave populations. These results are discussed with regard to the sources of energy or general ecological conditions present in caves, and to the differences in behavior or feeding skills known in cavefish.

Reinstatement of Eschatoporiini Blaisdell, 1906, a unique tribe of blind cavernicolous Tenebrionidae from California, with a new species from Napa County (Coleoptera, Tenebrionidae, Lagriinae)

The tribe Eschatoporini Blaisdell, 1906 is reinstated, based on molecular and morphological data, and the spelling corrected as Eschatoporiini. The tribe currently includes only the cave-dwelling genus Eschatoporis Blaisdell, 1906 from California, which is associated with underground aquifers. A second species of Eschatoporis is described from a cave in Napa County, California. The phylogenetic placement of Eschatoporiini within the Lagriinae is examined, and notes on the biology of Eschatoporis are provided.

Radon levels in Romanian caves: an occupational exposure survey

A comprehensive radon survey has been carried out in seven caves located in the western half of Romania's most significant karst regions. Touristic and non-touristic caves were investigated with the aim to provide a reliable distribution of their radon levels and evaluate the occupational exposure and associated effective doses. Radon gas concentrations were measured with long-term diffusion-type detectors during two consecutive seasons (warm and cold). All investigated caves exceed the European Union reference level of radon gas at workplaces (300 Bq/m³). The radon concentration in these caves ranges between 53 and 2866 Bq/m³, reflecting particular cave topography, season-related cave ventilation, and complex tectonic and geological settings surrounding each location. Relatively homogeneous high radon levels occur in all investigated touristic caves and in Tăuşoare and Vântului along their main galleries. Except for Muierii, in all the other caves radon levels are higher during the warm season, compared to the cold one. This suggests that natural cave ventilation largely controls the underground accumulation of radon. The results reported here reveal that the occupational exposure in Urşilor, Vadu Crişului, Tăuşoare, Vântului, and Muierii caves needs to be carefully monitored. The effective doses to workers vary between an average of 0.25 and 4.39 mSv/year depending on the measuring season. The highest values were recorded in show caves, ranging from 1.15 to 6.15 mSv/year, well above the European recommended limit, thus posing a potential health hazard upon cave guides, cavers, and scientists.

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle

BACKGROUND

Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline.

RESULTS

Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study.

CONCLUSION

The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.

Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae)

The genus Loxosceles Heinecken & Lowe, 1832 has 91 representatives in the New World. Despite medical relevancy, the taxonomy of the genus is poorly understood. South American Loxosceles were divided into four groups of species: laeta, spadicea, gaucho and amazonica; this last one has a single species, Loxosceles amazonica Gertsch, 1967. More recently, the natural occurrence of L. amazonica in the New World has been questioned, due to the strong morphological resemblance and close phylogenetic relationship with Old World species, mainly with Loxosceles rufescens (Dufour, 1820). Herein, L. amazonica is rediagnosed and its morphological variation and natural distribution discussed. Two new species closely related to it from northeastern Brazil are also described, Loxosceles willianilsonisp. n., from the state of Rio Grande do Norte, and Loxosceles muriciensissp. n., from the state of Alagoas. The relationships of these new species with L. amazonica and L. rufescens are discussed.

Safe caves and dangerous forests? Predation risk may contribute to salamander colonization of subterranean habitats

Recent studies suggest that many organisms actively colonize the subterranean environment to avoid climatic stress, exploit new ecological opportunities and reduce competition and predation. Terrestrial salamanders are known to colonize the more stable subterranean habitats mainly to escape external climatic extremes, while the role of predation avoidance remains untested. To better understand the importance of predation, we used clay models of the cave salamander Speleomantes strinatii to compare the predation occurring in woodland and subterranean habitats. Models were positioned in three forests and in three caves in NW Italy. One-hundred eighty-four models were retrieved from the field and 59 (32%) were attacked by predators. Models were attacked on their head more often than expected by chance and, therefore, were perceived by predators as real prey items. In the woodlands, clay models showed a four-time higher probability of being attacked in comparison to caves, suggesting a different level of potential predation risk in these surface habitats. These findings are one of the first experimental evidences that, in terrestrial ecosystems, predation avoidance may contribute to the salamander underground colonization process.

CO2 sequestration by ureolytic microbial consortia through microbially-induced calcite precipitation

Urea is an abundant nitrogen-containing compound found in urine of mammals and widely used in fertilizers. This compound is part of the nitrogen biogeochemical cycle and is easily biodegraded by ureolytic microorganisms that have the urease enzyme. Previous studies, with ureolytic isolates, have shown that some ureolytic microorganisms are able to sequester CO₂ through a process called microbially-induced calcium carbonate precipitation. The present study investigates 15 ureolytic consortia obtained from the "Pamukkale travertines" and the "Cave Without A Name" using different growth media to identify the possible bacterial genera responsible for CO₂ sequestration through the microbially-induced calcite precipitation (MICP). The community structure and diversity were determined by deep-sequencing. The results showed that all consortia presented varying CO₂ sequestration capabilities and MICP rates. The CO₂ sequestration varied between 0 and 86.4%, and it depended largely on the community structure, as well as on pH. Consortia with predominance of Comamonas, Plesiomonas and Oxalobacter presented reduced CO₂ sequestration. On the other hand, consortia dominated by Sporosarcina, Sphingobacterium, Stenotrophomonas, Acinetobacter, and Elizabethkingia showed higher rates of CO₂ uptake in the serum bottle headspace.

Life in a dark biosphere: a review of circadian physiology in "arrhythmic" environments

Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats. One of the least understood aspects of life in the dark biosphere is the rhythmicity of physiology and what it means to live in an environment of low or no rhythmicity. Here we describe methods that may be used to understand rhythmic physiology in the dark and summarise some of the studies of rhythmic physiology in "arrhythmic" environments, such as the poles, deep sea and caves. We review what can be understood about the adaptive value of rhythmic physiology on the Earth's surface from studies of animals from arrhythmic environments and what role a circadian clock may play in the dark.

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot

Caves in Mizoram, Northeast India, are potential hotspot diversity regions due to the historical significance of the formation of the Indo-Burman plateau and also because of their unexplored and unknown diversity. High-throughput paired end Illumina sequencing of the V4 region of 16S rRNA was performed to study the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (OTUs) (based on 97 % cutoff) comprising of 21 major and 21 candidate phyla with a sequencing depth of 1,140,013 were found in this study. The overall taxonomic profile obtained by the RDP classifier and Greengenes OTU database revealed high diversity within the bacterial communities. Communities were dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of Archaea were less varied and mostly comprising of Eukaryoarchea. Analysis revealed that Farpuk (CFP) cave sediment has low microbial diversity and is mainly dominated by Actinobacteria (80 % reads), whereas different bacterial communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis also revealed that a major portion of the identified OTUs was classified under rare biosphere. Importantly, all these caves recorded a high number of unclassified OTUs, which might represent new species. Further analysis with whole genome sequencing is needed to validate the unknown species as well as to determine their functional role.