Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy

The sulfide-rich Frasassi cave system hosts an aphotic, subsurface microbial ecosystem including extremely acidic (pH 0-1), viscous biofilms (snottites) hanging from the cave walls. We investigated the diversity and population structure of snottites from three locations in the cave system using full cycle rRNA methods and culturing. The snottites were composed primarily of bacteria related to Acidithiobacillus species. Other populations present in the snottites included Thermoplasmata group archaea, bacteria related to Sulfobacillus, Acidimicrobium, and the proposed bacterial lineage TM6, protists, and filamentous fungi. Based on fluorescence in situ hybridization population counts, Acidithiobacillus are key members of the snottite communities, accompanied in some cases by smaller numbers of archaea related to Ferroplasma and other Thermoplasmata. Diversity estimates show that the Frasassi snottites are among the lowest-diversity natural microbial communities known, with one to six prokaryotic phylotypes observed depending on the sample. This study represents the first in-depth molecular survey of cave snottite microbial diversity and population structure, and contributes to understanding of rapid limestone dissolution and cave formation by microbially mediated sulfuric acid speleogenesis.     

Influence of geomorphology and surface features on the genetic structure of an important trogloxene,the secret cave cricket (<Emphasis Type="Italic">Ceuthophilus secretus</Emphasis>)

Cave ecosystems supporting a variety of endemics depend on the carbon, nitrogen, and nutrients brought into caves by trogloxenic species, such as the secret cave cricket (Ceuthophilus secretus). Surface movements of trogloxenes may comprise the strongest ecological connections among caves. Our objective was to better understand dispersal patterns in C. secretus in order to inform management of this species and the cave endemics that depend upon them. We used microsatellite loci to estimate gene flow and genetic diversity among 42 karst features supporting C. secretus on the Fort Hood Military Reserve, Texas, USA. This sampling was used to assess the influences of karst topography and other landscape features on genetic diversity and population structure. Cave populations did not exhibit evidence of recent bottlenecks and genetic diversity was similar among sites, with the exception of one sample from an isolated cave. Samples exhibited a strong pattern of isolation by distance, but karst topology was also influential, with genetic differentiation being much higher between samples from separate ridges than among those on the same ridge. It appears that co-location on a ridge was an important factor facilitating dispersal among karst features. There was little evidence that other surface features such as forest cover, roads or streams influenced gene flow and genetic differentiation. The low genetic connectivity among ridges suggests that isolated caves on ridges where cricket habitat is uncommon or degraded might not be easily recolonized after extinction events, with potentially negative consequences for associated cave communities.     

岩画和壁画类文物微生物病害研究进展

古代岩画和壁画是人类文明发展历史进程的重要记录,具有极高的历史价值、艺术价值及科学价值,但他们无时无刻不受到环境因素引起的物理、化学及生物的劣化作用。近年,有关微生物对古代岩/壁画的危害逐渐受到关注。阐述了世界一些著名的岩/壁画文物的微生物的研究进展,如法国拉斯科洞穴岩画(Lascaux Cave)、西班牙阿尔塔米拉洞穴岩画(Altamira Cave)、敦煌石窟壁画、嘉峪关魏晋墓壁画以及我国东北地区公元5世纪的墓葬壁画等。通过对以上所述岩画和壁画微生物群落的分析比较,发现主要的细菌群落是变形菌门和放线菌门,放线菌门以假诺卡氏菌为主。真菌群落主要以虫生真菌为主。进一步分析了岩画和壁画微生物病害的共性和区别,揭示了洞穴、墓室等特殊环境下的微生物群落特点,为防治古代岩/壁画微生物病害提供了以下借鉴。     

贵州部分洞穴裸灶螽的鉴定及其遗传多样性分析

贵州是中国具有丰富喀斯特洞穴生态系统的省份之一,裸灶螽作为洞穴中的优势物种又为生态环境指示种,其遗传多样性能够反应洞穴生物多样性.为评估洞穴开发对洞穴生物多样性的影响,本研究通过形态鉴定和分子辅助鉴定的方式对来自贵州省毕节、黔西南、铜仁和黔南4个地区8个洞穴97号裸灶螽标本进行鉴定,并对其遗传多样性进行分析.结果共鉴定...     

Influence of vegetation regeneration and agricultural land use on lizard composition,taxonomic and functional diversity between different vegetation types in Caatinga domain,Brazil

Anthropogenic changes in habitats are one of the main threats to biodiversity. Understanding how species diversity and their functions are affected by these changes is crucial to assess environmental impacts. In this work, we aim to understand how lizard composition, taxonomic and functional diversity respond to differences in native vegetation regeneration stages (conserved vegetation and open secondary vegetation) and agricultural land use in different vegetation types (Caatinga sensu stricto, Cerrado sensu stricto and Relictual Humid Forest) in Caatinga domain, Brazil. In more degraded areas (open secondary vegetation and agricultural areas), we found a decline in species evenness, shown by greater dominance of few species. Moreover, we found a lower functional evenness in agricultural areas than in areas of conserved vegetation, which suggests that a smaller portion of functional traits present greater dominance in more anthropized areas. We did not detect any significant differences in species richness, but we did registered differences in species composition in Relictual Humid Forest. Contrary to our expectations, lizard abundance was also greater in more degraded areas, probably as a result of the increased abundance of species benefited by anthropization. In this work, we advance the knowledge of how anthropogenic changes influence lizard diversity and emphasize the importance of analysing different facets of diversity and different habitat environments to understand how anthropization affects patterns in community ecology.     

Fish Assemblages of Mediterranean Marine Caves

Fish assemblages associated with 14 marine caves and adjacent external rocky reefs were investigated at four Marine Protected Areas (MPAs) along the coasts of Italy. Within the caves sampling was carried out in different sub-habitats: walls, ceilings, bottoms and ends of caves. On the whole, 38 species were recorded inside the 14 caves investigated. Eighteen species were exclusively found inside the caves: they were mainly represented by speleophilic (i.e. species preferentially or exclusively inhabiting caves) gobids (e.g. Didogobius splechtnai) and nocturnal species (e.g. Conger conger). Forty-one species were censused outside, 20 of which were shared with cave habitats. Apogon imberbis was the most common fish found in all 14 caves investigated, followed by Thorogobius ephippiatus (recorded in 13 caves), and Diplodus vulgaris and Scorpaena notata (both censused in 12 caves). Distinct fish assemblages were found between external rocky reefs and the different cave sub-habitats. New data on the distribution of some speleophilic gobids were collected, showing the existence of a pool of species shared by marine caves on a large scale (i.e. hundreds of km). Considering the uniqueness of cave fishes (18 exclusive species and different assemblage structures), the inclusion of marine caves among the habitats routinely investigated for fish biodiversity monitoring could facilitate the achievement of more comprehensive inventories. Due to their contribution to local species diversity and the shelter they provide to species valuable for conservation, marine caves should be prioritized for their inclusion not only within future MPAs through the Mediterranean Sea, but also into larger management spatial planning.     

The depositional context of the early upper paleolithic human fossils from the Koneprusy (Zlatý kůn) and Mladec caves, Czech republic

The caves of Mladec I and II (Moravia) and Koneprusy (Bohemia) are principal hominid Early Upper Paleolithic sites in Central Europe that require a complex reconsideration from several viewpoints. The focus of this paper is on the depositional context of human fossils, which is clearer from the documentation of Koneprusy, excavated during the 1950s, than from the early reports about Mladec. Both caves are multi-floor underground karstic systems penetrated by vertical fissures and chimneys, where the fossils were found in restricted areas, related to debris cones accumulated under the chimneys. These associations are confirmed using Surfer reconstruction of the original fillings. It appears certain for Koneprusy and highly probable for Mladec that the fossils fell in through the chimneys. This does not mean that living animals and humans never entered the interior of the caves (traces of gnawing by hyenas are visible), but it makes it unlikely that the human paleontological accumulations were the result of human activity within the cave chambers.     

ECOMORPHOLOGICAL CONVERGENCE OF CAVE COMMUNITIES

Extreme selective environments are commonly believed to funnel evolution toward a few predictable outcomes. Caves are well‐known extreme environments with characteristically adapted faunas that are similar in appearance, physiology, and behavior all over the world, even if not closely related. Morphological diversity between closely related cave species has been explained by difference in time since colonization and different ecological influence from the surface. Here, we tested a more classical hypothesis: morphological diversity is niche‐based, and different morphologies reflect properties of microhabitats within caves. We analyzed seven communities with altogether 30 species of the subterranean amphipod (crustacean) genus Niphargus using multivariate morphometrics, multinomial logit models cross‐validation, and phylogenetic reconstruction. Species clustered into four distinct ecomorph classes—small pore, cave stream, cave lake, and lake giants—associated with specific cave microhabitats and of multiple independent phylogenetic origins. Traits commonly regarded as adaptations to caves, such as antenna length, were shown to be related to microhabitat parameters, such as flow velocity. These results demonstrate that under the selection pressure of extreme environment, the ecomorphological structure of communities can converge. Thus, morphological diversity does not result from adaptive response to temporal and ecological gradients, but from fine‐level niche partitioning.     

贵州仙家洞和忆苦洞洞穴动物群落多样性及其环境因子的影响

为了解矿区洞穴动物群落多样性特征及其影响因素,于2019年3月对贵州松桃锰矿区仙家洞和忆苦洞的动物进行了调查,运用主成分(PCA)综合分析了环境因子对洞穴动物群落多样性的影响,并利用潜在生态危害指数对洞穴内土壤重金属的生态风险水平进行了评价.结果 表明:共获动物标本445号,隶属4门8纲18目32科,其中仙家洞178号...     

Microbial Biomineralization in Biotic Crusts from a Pleistocene Marine Cave (NW Sicily,Italy)

Biotic crusts occurring in the Early Pleistocene Rumena Cave, in NW Sicily, have been analyzed from a geomicrobiological point of view. The crusts consist largely of scleractinians and of subordinate bryozoans and serpuloideans, all typical of submarine cave biota. Encrustations document a blind cave in a shadowed setting, or possibly below the fair weather swell zone. Autochthonous and, subordinately, detrital fractions were observed within the skeletal framework of biotic crusts. The syndepositional lithified fraction occurs mainly as very fine-grained laminations. Clotted peloidal and aphanitic (structureless) textures occur in the micrites as well. Autochthonous micrite is always associated with a significant amount of organic matter remains. In caves from the Plemmirio area in SE Sicily, the autochthonous microbial micrite, occurring in the bioconstructions, contains bacterial lipid biomarkers, including abundant compounds derived from sulfate-reducing bacteria. It is likely that a similar microbial mediation was involved in the formation of the autochthonous micrite present in the biotic crusts of the Rumena Cave.     

中国喀斯特洞穴维管植物多样性

洞穴是喀斯特景观中普遍存在的地质地貌结构, 拥有丰富的植物资源。仅2001-2020年间, 就发表了中国喀斯特洞穴维管植物新属1个; 新种(含种下等级) 170个, 隶属于16科31属, 占近20年发表的中国维管植物新种的3.9%, 说明洞穴植物具有较高的物种多样性潜力。据统计, 中国喀斯特洞穴维管植物有110科339属871种, 主要分布于广西、广东、贵州、云南、重庆等地。物种数排名前5的科包括苦苣苔科、荨麻科、鳞毛蕨科、秋海棠科和茜草科, 其所含物种数共占整个洞穴植物种类的39.4%; 排名前5的属包括报春苣苔属(Primulina)、楼梯草属(Elatostema)、耳蕨属(Polystichum)、秋海棠属(Begonia)和凤尾蕨属(Pteris), 其所含物种数共占整个洞穴植物种类的25.1%。本名录的所有洞穴植物中, 草本习性的种类占一半以上。从洞内分布来看, 仅有10.7%的种类分布于弱光带, 其中石松类和蕨类植物占比远高于被子植物, 说明前者更能适应弱光带的极端环境。不仅如此, 洞穴维管植物也具有较高的特有性成分, 其中省级特有种占比25.8%, 分别包括非洞穴特有种(11.0%)、多洞穴特有种(3.3%)和单洞穴特有种(11.5%)。依据文献显示受威胁种类有115种(占13.0%)。受威胁种类占比较高的类群均是近年来发表新种较多的科, 包括鳞毛蕨科、苦苣苔科、荨麻科、秋海棠科、茜草科等。针对这些类群, 有待更详细地调查来完善对它们的评估。此外, 本名录中至少有36%的种类没有任何分子数据, 亟待补充。     

Recently discovered landlocked basins in Indonesia reveal high habitat diversity in anchialine systems

In this article, the variability of physical settings of anchialine systems in Indonesia is discussed together with the consequences these settings have for the environment and biota within the systems. Exploration in two karstic areas (Berau, East Kalimantan and Raja Ampat, West Papua) has resulted in the discovery of 20 previously unknown anchialine systems in Indonesia. Based on parameters such as bathymetry, size, coastline, salinity, water temperature, pH, degree of connection to the sea, and the presence-absence of selected key taxa we distinguish three types of (non-cave) anchialine systems in the Indo-Pacific: (1) Marine lakes with large and deep basins containing brackish to almost fully marine waters. Marine lakes show a range in the degree of connection to the sea with the result that the higher the connection the more the lake resembles a lagoon in both water chemistry and biota, while the more isolated lakes have brackish water and contain unique species that are rarely found in the adjacent sea. (2) Anchialine pools with small and shallow basins containing brackish water and low diversity of macrofauna. (3) Blue pools in chasms that contain water with a clear halocline and are possibly connected to anchialine caves. Study of the many unique features of anchialine systems will enhance our understanding of the physical and ecological processes responsible for diversification in tropical shallow marine environments.     

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are “evolutionary dead‐ends.” This implies that cave‐adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave‐dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave‐dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave‐dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a “dead‐end” for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.     

Cave lithology determining the structure of the invertebrate communities in the Brazilian Atlantic Rain Forest

In Brazil, only limestone caves and a few caves in sandstone, iron ore and granite rocks had their invertebrate communities evaluated. Being such, the present study aimed to promote a comparative analysis of the structure of the invertebrate communities in caves associated to carbonatic, magmatic, siliciclastic and ferruginous rocks of the Brazilian Atlantic forest. Significant differences in the relative richness, abundance and diversity were observed between lithologies. The average relative richness was higher in the ferruginous caves (0.53 spp). The total number of troglomorphic species was significantly different among caves and the highest average richness occurred at ferruginous caves (5.79 spp/cave). Siliciclastic, carbonatic and magmatic caves presented a higher quantitative similarity of the fauna. Ferruginous caves revealed communities with a fauna composition different from the other lithologies. The total richness of invertebrates correlated significantly and positively with the linear development in the siliciclastic caves (R_s = 0.67, P < 0.05), carbonatic (R_s = 0.71, P < 0.05) and ferruginous (R_s = 0.74, P < 0.05). The rock type in which the cave is inserted can determine differences in the richness of invertebrate troglophyles and troglobites. Therefore, on creating value attributes, the size of the caves should always come related to their lithology by the fact that same sized caves associated to different lithologies, possess communities with quite diverse structures.     

Uncovering the origin of the black stains in Lascaux Cave in France

Lascaux Cave in France was discovered in 1940. Since being opened to visitors the cave has suffered three major microbial outbreaks. The current problem is the fast dissemination of black stains which are threatening the Palaeolithic paintings. Previous data pointed to the involvement of new fungal species in the formation of black stains on the rock walls and ceiling. However, it appears that there could be other reasons for the formation of different and extensive black stains coating the surface of the clayey sediments. Our analyses reveal that black stains on clayey sediments are mainly produced by Acremonium nepalense, a manganese oxide‐depositing fungus, widely distributed in the cave. Thus, in Lascaux Cave, the black stains have a dual origin: on limestone rocks they are mainly produced by the accumulation of fungal melanins, and on clayey sediments by the biogenic deposition of black manganese oxides.     

Diversity and ecology of the bryophytes in the cave environment: a study on the volcanic and karstic caves of Sicily

The results of a long investigation (20 years) on bryophyte diversity of 28 Sicilian caves are reported; the study regarded both karstic and volcanic caves, located at altitudes ranging from 15 to 2030 m a.s.l. The bryophyte diversity consists of a total of 136 taxa, 20 liverworts, 3 hornworts and 113 mosses. The ecological analysis was performed using the Ellenberg indicator values for moisture, light and soil reaction to the substrate. On the whole, mesophytic and meso-hygrophytic, sciophytic and photo-sciophytic species strongly prevail independently from the geological nature of the caves; the values of the soil reaction to the substrate well reflect the characteristics of the substrate. The phytogeographical analysis shows the prevalence of the Mediterranean species, followed by the temperate and southern-temperate species. It is remarkable the occurrence of boreo-arctic-montane species, which find refuge for their survival in some high-altitude caves. Some typical species well adapted to the cave environment are reported, including Amphidium mougeotii, Isopterygiopsis pulchella, Thamnobryum alopecurum and Rhynchostegiella tenella, showing a troglophilous character. The occurrence of species of phytogeographical significance, as well as of conservation interest, e.g. Ptychostomum cernuum, Tortula bolanderi, Rhabdoweisia fugax, Grimmia torquata, Brachytheciastrum collinum, very rare in Italy, is emphasized too.     

Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time

The cave bear spread from Western Europe to the Near East during the Riss glaciation (250 KYA) before becoming extinct approximately 12 KYA. During that period, the climatic conditions were highly dynamic, oscillating between glacial and temperate episodes. Such events have constrained the geographic repartition of species, the movements of populations and shaped their genetic diversity. We retrieved and analyzed ancient DNA from 21 samples from five European caves ranging from 40 to 130 KYA. Combined with available data, our data set accounts for a total of 41 sequences of cave bear, coming from 18 European caves. We distinguish four haplogroups at the level of the mitochondrial DNA control region. The large population size of cave bear could account for the maintenance of such polymorphism. Extensive gene flow seems to have connected European populations because two haplogroups cover wide geographic areas. Furthermore, the extensive sampling of the deposits of the Scladina cave located in Belgium allowed us to correlate changes in climatic conditions with the intrapopulational genetic diversity over 90 KY.     

Upper Pleistocene Panthera leo spelaea (Goldfuss, 1810) remains from the Bilstein Caves (Sauerland Karst) and contribution to the steppe lion taphonomy,palaeobiology and sexual dimorphism

Remains of the steppe lion Panthera leo spelaea (Goldfuss) from historical digs in the Bilstein Caves of Warstein (Sauerland, NW Germany) are described. Their age seems to be from the Early Weichselian periods (Upper Pleistocene). Whereas the Bilstein cave was inhabited by cave bears at that time only a few hyena prey remains, were most likely imported into the cave entrance by hyenas. Bite and crush marks on a few bones of Bison priscus, Bos primigenius, Cervus elaphus, a rhinoceros Coelodonta antiquitatis vertebra and even several chewed cave bear bones prove the hyena presence which is similar to other caves in the Sauerland hyena den cave rich region. Additionally some larger wolves subspecies Canis lupusspelaeus bones were found, but only few Crocuta crocuta spelaea remains are present. After taphonomic comparisons to six other hyena and cave bear den caves of northern Germany, this cave can be classified as a cave bear den, which was briefly used by hyenas only for food storage or commuting or cave bear predation site in one part of the Cave. The lion material refers at least to one young adult lioness, one more adult female and two male lions; therefore, at minimum, the remains of four adult individuals are represented. The absence of juvenile lion material, in contrast to cave bear cub remains in the Bilstein Caves, proves that P. leo spelaea did not use this and all other caves in the region to raise their cubs. The bone material from the Bilstein Caves would prove the same hyena-lion antagonism conflict being recently proven for the Perick Caves, Balve Cave or Martins Cave well. Other situations in caves such as the Keppler Cave and the Bilstein Cave initially show the more complex taphonomic situation of lion remains in European caves, especially in cave bear dens, where they seem to have hunted periodically cave bears, such as it is already proven for hyenas in the Sauerland Karst and other caves of Europe.     

Aerobiology: An ecological indicator for early detection and control of fungal outbreaks in caves

Aerobiology of caves is still in its infancy. At present, no clear information has been generated on the limits of acceptance of fungal spores in air which permit classification of the atmosphere of a cave as not dangerous for the conservation of rock-art paintings. We had the unique opportunity to visit and sample different caves in Spain and France, under different managements. We obtained a collection of data related with contamination episodes that permitted the formulation of a tentative index of fungal hazard in show caves. This is supported by the concentration of fungal spores in the cave air, the knowledge of the cave history and management, and a detailed survey of the different halls of the caves. The index classifies the risks into five categories: category 1 identifies a cave without fungal problems, category 2 is an alarm signal for caves, category 3 is a cave threatened by fungi, category 4 is assigned to a cave already affected by fungi, and category 5 is a cave with an irreversible ecological disturbance. This index, a working hypothesis, is launched to promote interest and forum discussion and should be validated by the scientific community after being updated with more surveys and cave analyses carried out under different managements and with different contamination episodes.