Caves are ecosystems and natural heritage sites with magnificent biological diversity, from microorganisms to animals, despite their selective environment for development and survival. Until now, studies on cave microbiomes have included taxonomic classification through metagenomics analysis, demonstrating microbiological heterogeneity mainly composed of prokaryotic organisms or bacteria species. The generally oligotrophic environment, with limited energy input and dark zone, is the main feature differentiating the cave microorganisms from the other microbiomes and resulting in a unique habitat, which has unexplored regard to biology and chemical diversity. Multi-omics integration is a key strategy for scanning and integrating the macro and micromolecular universe, providing a better comprehension of processes and answers of the microbiome in natural cavities. Here, we highlight the strategies employed to study the cave microbiome, from the microbial genomes to their ability to secondary metabolites production, and also the multi-omics integration to explore the chemical and biological diversity in caves. animals survival now analysis species zone habitat Multiomics Multi omics universe cavities Here production multiomics multi caves

ABSTRACT Pseudochthonius lubueno sp. nov., a new obligatory cave-dwelling pseudoscorpion species is described from Gruna da Altina cave, the fifth species of the genus in the region of Serra do Ramalho karst area, southwestern Bahia, Brazil. This genus occurs in South and Central America, sub-Saharan central Africa, and in the Arabian Peninsula. The new species can be identified by the following combination of characters: eyes or eyespots absent, coxa I with two and coxa II with 4-5 coxal spines, without microdenticles on the fixed pedipalpal finger, rallum with five blades, ratio ist-est/ist-esb = 1.9. With this new description, the genus now includes 15 species from Brazil: P. biseriatus Mahnert, 2001, P. brasiliensis Beier, 1970, P. diamachi Prado & Ferreira, 2023, P. gracilimanus Mahnert, 2001, P. heterodentatus Hoff, 1946, P. homodentatus Chamberlin, 1929, P. koinopoliteia Prado & Ferreira, 2023, P. lubueno sp. nov., P. orthodactylus Muchmore, 1970, P. olegario Schimons ky, 2022, P. pali Prado & Ferreira, 2023, P. ramalho Assis, Schimonsky & Bichuette, 2021, P. ricardoi Mahnert, 2001, P. strinatii Beier, 1969 and P. tuxeni Mahnert, 1979. The new species shows troglomorphic characteristics such as the depigmentation of the carapace and the absence of eyes. In addition, illustrations, diagnoses, an identification key for cave-dwelling species of the genus, and distribution maps for all Brazilian species of Pseudochthonius are provided.

Abstract The present work aims to describe the first troglobitic terrestrial isopod (Oniscidea) from Peru. Caecopactes chullachaqui sp. nov. is described from Cueva de Palestina, Department of San Martín. The new species constitutes the third troglobitic taxon known for the country and extends the knowledge of the distribution of the genus. Oniscidea (Oniscidea Peru sp nov Palestina Martín genus

Abstract We propose a new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975, with data on its distribution, ecology, aspects of behavior, and conservation status. Spelaeogammarus ginae sp. nov. occurs in a single cave in the Serra do Ramalho karst area, of the northeastern Brazilian semi-arid region. We also provide new data on the distribution and conservation status of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000 that occurs in the upper phreatic aquifer inside caves from Chapada Diamantina domain. Both species occur in caves in the state of Bahia, northeastern Brazil.

Resumo O presente trabalho traz informações sobre as ameaças aos peixes subterrâneos no Brasil. Atualmente, são conhecidas pelo menos 36 espécies, 22 das quais já foram formalmente descritas. O endemismo é a regra para a maioria destas espécies. Em relação à conservação, esses peixes são em geral considerados ameaçados: a maioria das espécies já descritas está incluída em listas regionais de fauna ameaçada e apenas quatro delas estão incluídas na lista global da IUCN. Em relação aos habitats, os peixes subterrâneos brasileiros ocorrem em sedimentos aluviais (parte da zona hiporreica), riachos de nível de base, cavernas inundadas, lagos no lençol freático, tributários vadosos superiores e aquíferos no epicarste. Detectamos onze ameaças principais, a maioria relacionada à agricultura, pecuária e projetos hidrelétricos, entretanto, turismo sem planos de manejo e poluição também representam ameaças significativas. Duas ameaças afetam um grande número de espécies: a mudança física do habitat e a restrição de alimento. As bacias hidrográficas com o maior número de ameaças identificadas são a do alto Tocantins (oito) seguida pela do alto Paraguaçu (seis). Propostas eficazes para proteger esse componente negligenciado da biodiversidade brasileira são ainda escassos, como os projetos de monitoramento e sua função nas comunidades subterrâneas, além de projetos relacionados à educação, visando a sensibilização do público.

Abstract The present work brings information on threats to the subterranean fishes in Brazil. Currently, at least 36 species are known, 22 of which are already formally described. Endemism is the rule for most of them. Regarding their conservation, these fishes are in general considered threatened: and most of the already formally described species are included in national lists of threatened fauna, and only four of them are included in the global list of the IUCN. Regarding habitats, Brazilian subterranean fishes occur in alluvial sediments (part of the hyporheic zone), shallow base-level streams, flooded caves, lakes in the water table, upper vadose tributaries, and epikarst aquifers. We detected 11 main threats, mainly related to agriculture, pasture, and hydroelectric plans, but unmanaged tourism and pollution are also significant threats. Two threats affect a high number of species (physical change of the habitat and food restriction). The river basins with the higher number of identified threats are the upper Tocantins (eight) followed by the upper Paraguaçu (six). Effective proposals to protect this neglected component of the Brazilian biodiversity are still scarce, such as monitoring projects and their function in the subterranean communities, besides education projects aiming to develop public awareness.

Resumo: Fatores limitantes dos ambientes subterrâneos como alta umidade relativa do ar e, principalmente, a falta de luz, representam filtros ecológicos para organismos e padrões de biodiversidade de comunidades superficiais e subterrâneas, nas quais mostram grandes disparidades. Diversidade e singularidade subterrâneas são, portanto, mais bem expressas quando os presença de espécies raras e endêmicas. Nosso estudo teve como objetivo descrever a diversidade da fauna da caverna de 14 cavernas do Parque Nacional das Cavernas de Peruaçu (PCNP), leste do Brasil. Analisamos a diversidade regional usando o índice que inclui a distinção taxonômica média (TD - Δ +, AvTD). Registramos 1,674 indivíduos pertencentes a 10 classes e 237 morfotipos, 11 troglóbios e dois troglomórficos e possíveis troglóbios. A maior abundância de espécies (N = 330) e riqueza (s = 76) foram registradas na caverna da Lapa do Cipó, seguida por Gruta Olhos d´Água (N = 330, s = 71), que mostra o maior valor de DT (Δ + = 90,18) em relação aos outros, incluindo a Lapa do Cipó mais rica (Δ + = 85,24), consequência das várias unidades taxonômicas com grande número de espécies. Os valores abaixo do esperado de TD (Δ + = 87,70) podem indicar impactos antrópicos nessas comunidades. Nossos resultados demonstram que as cavernas Gruta Olhos d ‘Água e Lapa do Cipó são os locais mais importantes para a ocorrência de espécies endêmicas e troglóbias e pode fazer parte de um sistema complexo que deve ser considerado por mais planejamento eficiente de conservação.

Abstract: Limiting factors of subterranean environments, high relative air humidity and, especially, permanent darkness, represent ecological filters for organisms and biodiversity patterns of surface and subterranean communities display wide disparities. Subterranean diversity and singularity are, thus, better expressed when the common presence of rare and endemic species are considered. Our study aimed to describe the diversity of the cave fauna from 14 caves from Peruaçu Caves National Park (PCNP), eastern Brazil. We analyzed the regional diversity using the index that includes the average taxonomic distinction (TD - Δ +, AvTD). We recorded 1,674 individuals belonging to 10 Classes and 237 morphotypes, 11 troglobitic and two troglomorphic and possible troglobites. Greatest species abundance (N=330) and richness (s=76) were recorded at Lapa do Cipó cave, followed by Gruta Olhos d’Água (N=330, s=71), which shows the highest TD value (Δ + = 90.18) in relation to the others, including the richest Lapa do Cipó (Δ + = 85.24), consequence of the several taxonomic units with large number of species. The below-expected values of TD (Δ + = 87.70) may indicate anthropic impacts on these communities. Our results demonstrate that Gruta Olhos d’ Água and Lapa do Cipó caves are the most important sites for the occurrence of endemic and troglobitic species and may be part of a complex system that should be considered for a more efficient conservation planning.

ABSTRACT The food base in the subterranean environment consists mainly of allochthonous materials. In this environment the resources are distributed generally in a heterogeneous dispersed way and the distribution of resources and their availability determine where the terrestrial invertebrates will reside, which is important for understanding ecological relationships and to establish conservation strategies. Thus, we tested how the complexity of substrates influences the richness and composition of the subterranean terrestrial invertebrates in the Presidente Olegário karst area, southeastern Brazil. We carried out collections in six caves during both dry and wet seasons, using combined collection methods. We observed different distributions in relation to the substrate, because the environmental heterogeneity increases the amount of available niches for the fauna. Some taxa showed a preference for specific substrates, probably related to the availability of food resources and humidity and to body size restriction, emphasizing the niche differentiation between species. Anthropogenic impacts can cause irreversible alterations in the subterranean fauna because the subterranean environment is dependent on the surface for input of trophic resources. On-going impacts in the Presidente Olegario karst area, like agriculture, pastures, gas extraction, and hydroelectric projects, are therefore a serious threat to subterranean biodiversity and this region should be prioritized for conservation.

ABSTRACT We describe for the first time the adult female of the troglobitic scorpion Troglorhopalurus translucidus Lourenço Baptista & Giupponi, 2004, and broaden its known distribution to other sandstone caves at Chapada Diamantina's region. The life history of T. translucidus is reconstructed through morphometric measurements, with a multivariate analysis applied on a set of 16 specimens in all stages (including the holotype) and biological notes. The ontogeny of T. translucidus has seven stages and the litter size is 43 (n = 1). We discuss the isolation of T. translucidus and Rhopalurus lacrau Lourenço & Pinto-da-Rocha, 1997 in caves of Chapada Diamantina, and discuss their troglomorphisms (autapomorphies) among other species related with Rhopalurus . Both species must be considered fragile due their restricted endemism at Chapada Diamantina.

ABSTRACT A second amphibian species of terrestrial isopods in the genusXangoniscus Campos-Filho, Araujo & Taiti, 2014 and two new species of Trichorhina Budde-Lund, 1908 are described from the Bambuí karst area in the state of Minas Gerais. Xangoniscus odara n. sp. and Trichorhina cipoensis n. sp. were collected in Lapa do Cipó cave, municipality of Itacarambi, andTrichorhina pataxosi n. sp. in Gruta do Sufoco and Gruta do Nei, municipality of Pedro Leopoldo.

Resumo No presente estudo analisamos a assembleia de morcegos da caverna granítica Gruta do Riacho Subterrâneo e sua área de entorno (Itu, estado de São Paulo, Brasil) com o objetivo de verificar a influência da sazonalidade na composição de espécies e na abundância das populações. Foram realizadas cinco amostragens com duração de três dias cada, ao longo do período de outubro de 2013 a setembro de 2014, utilizando redes-de-neblina instaladas nas entradas, no interior da caverna e em seu entorno, totalizando um esforço de captura de 6.090 m2.h. Nossos resultados indicam que esta caverna abriga uma assembleia rica, onde foram capturadas quinze espécies. Carollia perspicillata, Desmodus rotundus e Myotis sp. foram as espécies mais abundantes. A comparação da composição desta assembleia com a de outras cavernas do estado de São Paulo revelou que suas espécies são similares e típicas da quiropterofauna de cavernas da Mata Atlântica, independentemente da litologia das mesmas. A análise de regressão múltipla utilizada para a relação entre a variação sazonal das variáveis temperatura, pluviosidade e umidade relativa do ar não revelou correlação significativa entre estas e as variações na abundância das diferentes espécies de morcegos. Contudo a análise de correspondência canônica incluindo, além destas, a variável luminosidade da lua indicou uma correlação significativa com a umidade relativa do ar. As variações nas abundâncias dos morcegos provavelmente estão relacionadas à sazonalidade na disponibilidade de alimento. A curva de acumulação obtida pela relação entre a riqueza de espécies e o número de amostragens acumuladas mostrou que mais amostragens são necessárias para atingir a assíntota da riqueza de espécies. Considerando-se que a Gruta do Riacho Subterrâneo é a maior caverna granítica do Brasil e que abriga uma elevada riqueza de espécies de morcegos, incluido raras e comuns, nós sugerimos a preservação desta caverna para a manutenção da diversidade morcegos no estado de São Paulo.

Abstract In the present study we analyzed the bat assemblage of the granitic cave Gruta do Riacho Subterrâneo and its surroundings (Itu, São Paulo state, Brazil) aiming to verify the influence of seasonality on its species composition and population abundances. Five samplings were carried out with three days of duration each, along the period from October 2013 to September 2014. Captures of bats were performed by setting mist nets in cave entrances, its interior and surroundings, making a total capture effort of 6,090 m2.h. Our results indicate that this cave is shelter for a rich bat assemblage with fifteen species captured. Carollia perspicillata, Desmodus rotundus and Myotis sp. were the most abundant species. A comparison of the assemblage composition with that of other caves of São Paulo state revealed that its composition is very similar and typical of the Atlantic Forest Atlantic cave chiropterofauna independently of cave lithology. A multiple regression analysis performed to check for the existence of correlation between the seasonal fluctuation of the climatic variables temperature, pluviosity and air humidity did not reveal significant relationships among these and the changes in the abundance of bats. However, the analysis of canonical correspondence including these variables and also moonlight luminosity indicated a significant relationship of the changes in bat abundance with the air relative humidity. Changes in bat abundances are probably related to the seasonality in food availability. The accumulation curve obtained from the relationship between the accumulated richness of species and the number of samples showed that more samplings are required to reach the asymptote of species richness. Considering that Gruta do Riacho Subterrâneo is the largest granitic cave in Brazil and that it shelters a high number of bat species, including common and rare species, we suggests the preservation of this cave for maintenance of bat diversity in São Paulo state.

O peixe troglóbio Eigenmannia vicentespelaea, endêmico de um único sistema de cavernas e incluído na Lista Brasileira de Fauna Ameaçada foi estudado em relação às densidades populacionais e hábitat. Para comparação utilizamos a espécie epígea E. trilineata. Verificamos se as densidades populacionais registradas para E. vicentespelaea seguem o padrão observado para outros peixes subterrâneos; se há flutuações sazonais nestas densidades e quais variáveis ambientais explicam as variações nas densidades. Estimamos as abundâncias e densidades populacionais ao longo de três estações secas consecutivas, concomitantes à descrição do habitat e das variáveis físico-químicas. Para E. vicentespelaea: em seis trechos de rio ao longo da caverna São Vicente II. Para E. trilineata: na contagem de peixes ativos no rio da Lapa. A densidade populcional média registrada para E. vicentespelaea é baixa (0,17 ind.m-2), similar à observada para E. trilineata (0,13 ind.m-2), sem diferenças significativas entre os anos, mas com flutuações marcantes ao longo das estações secas dentro de cada ano, sugerindo sazonalidade. O tamanho populacional estimado para E. vicentespelaea é considerado pequeno (270 indivíduos em média). Profundidade, correnteza, substrato, aliadas à concentração de detrito vegetal explicam melhor a variação nas densidades. Ações urgentes para conservação de E. vicentespelaea incluem a proteção das nascentes do Parque Estadual de Terra Ronca.

The troglobitic electric fish Eigenmannia vicentespelaea, endemic to a single cave-system and included in the Brazilian Red List of Threatened Fauna, was studied in relation to population densities and habitat. For comparison, we used the epigean species, E. trilineata. We verify if the population densities recorded for E. vicentespelaea follow the pattern observed for other subterranean fishes; if there are seasonal fluctuations in these densities and which environmental variables explain the densities variation. We estimated abundances and population densities during three consecutive dry seasons concomitant with habitat description and physicochemical variables measurements. For E. vicentespelaea: in six stream reaches in the São Vicente II cave. For E. trilineata: from counts of active fish in rio da Lapa. The mean population density recorded for E. vicentespelaea is considered low (0.17 ind.m-2), similar to those of E. trilineata (0.13 ind.m-2), without significant differences between the years, but with marked fluctuations during dry seasons within each year, suggesting seasonality. Estimated population size of E. vicentespelaea is considered low (270 individuals in average). Depth, water current and substrate, allied to plant debris explain better the variation of densities. Urgent actions for E. vicentespelaea conservation include protection of headsprings in Terra Ronca State Park.

Subterranean environments, even though they do not possess a primary production (photosynthesis), may present high biodiversity, faunistic originality, endemism, phylogenetic isolations and unique ecological and/or evolution events, in addition to rare taxa. Studies investigating the biological diversity in Neotropical caves are relatively rare and recent, and most of them have been conducted in Brazil. We sampled caves from the state of Bahia, northeastern Brazil, and through sampling sufficiency tests and richness estimators, we demonstrate that the normatization for the Brazilian cave laws is not adequate for its conservation and that only α diversity index is not enough to verify faunistic patterns. We suggest that a phylogenetic diversity index be more robust and accurate for conservation purposes, particularly the Taxonomic Distinctness index. Moreover, we propose that the sandstone complex caves from Chapada Diamantina National Park need to be classified as being of high subterranean biodiversity in a global scope.

A new subterranean and troglomorphic species of Ituglanis Costa and Bockmann, 1993 is described from the carbonatic karst area of northeastern Goiás state, upper Tocantins River Basin, central Brazil, representing the sixth subterranean species of the genus described from the same region. Ituglanis boticario sp. nov. is diagnosed by a combination of unusual characters for the genus: body pigmentation forming longitudinal stripes, 7-8 pairs of ribs, presence of the anterior segment of the infraorbital laterosensory canal, and usually 8 pectoral-fin rays. Due to the absence of epigean populations and the presence of some degree of morphological specialization to the subterranean environment, it can be classified as a troglobite (i.e., exclusively subterranean). The description of this species increases the importance of the northeastern Goiás region as a biodiversity spot for subterranean ichthyofauna, mainly Ituglanis. The region demands urgent political efforts to ensure the preservation of its speleobiological patrimony, including the Tarimba cave system, one of the largest caves in Brazil and type-locality of I. boticario sp. nov.

Uma nova espécie de Tmesiphantes Simon, 1892, é descrita em cavernas areníticas/quatzíticas da Chapada Diamantina, estado da Bahia, Brasil. Essa é a quinta espécie do gênero e o primeiro registro de uma migalomorfa troglóbia do Brasil. É apresentada chave de identificação para todas as espécies de Tmesiphantes.

A new species of Tmesiphantes Simon, 1892, is described from sandstone/quartizitic caves of Chapada Diamantina, Bahia State, Brazil. This is the fifth species of the genus and the first record of a troglobitic mygalomorph in Brazil. A key is presented for all Tmesiphantes species.

Trichomycterus dali, espécie nova, é descrita de cavernas calcárias alagadas na área cárstica da Serra da Bodoquena, estado do Mato Grosso do Sul, Brasil central. A nova espécie é diagnosticada por um caráter único no gênero, a presença de dobras adiposas conspícuas, em forma de crista, passando por toda a região dorsal do corpo. Trichomycterus dali pode ser ainda diferenciada facilmente de suas congêneres epígeas pela redução dos olhos e da pigmentação cutânea (exceto para T. gorgona), e das congêneres restantes (isto é, todas as hipógeas mais T. gorgona) pela perda total dos olhos, não visíveis externamente (exceto para T. sandovali e T. spelaeus). Outras características diagnósticas incluem barbilhões muito longos, especialmente o nasal (99,3-143,5% do comprimento da cabeça) e o maxilar (97,0-131,3% do comprimento da cabeça), contagem de raios da nadadeira peitoral atingindo I,9 e uma fontanela cranial única com uma constrição conspícua no ponto de encontro do supraoccipital e dos dois ossos frontais. O status troglóbio da espécie é sugerido pela presença de troglomorfismos em avançado grau, especialmente a redução da pigmentação cutânea, a perda total dos olhos e os barbilhões alongados. Além disso, a presença de uma dobra adiposa bem desenvolvida nos adultos pode indicar uma adaptação distintiva, adquirida por neotenia, para enfrentar as condições alimentares escassas do seu habitat hipógeo.

Trichomycterus dali, new species, is described from flooded limestone caves in Serra da Bodoquena karst area, State of Mato Grosso do Sul, Central Brazil. The new species is diagnosed by a unique character in the genus, the presence of conspicuous, ridge-like adipose folds lining dorsally throughout the body. Trichomycterus dali can be further distinguished readily from epigean congeners by the reduction of eyes and skin pigmentation (except for T. gorgona), and from remaining congeners (i.e., all hypogean plus T. gorgona) by the total loss of eyes, not visible externally (except for T. sandovali and T. spelaeus). Other diagnostic features includes very long barbels, especially the nasal (99.3-143.5% HL) and the maxillary (97.0-131.3% HL), pectoral-fin ray count reaching I,9 and a unique cranial fontanel with a conspicuous constriction on the meeting point of supraoccipital and the two frontal bones. The troglobitic status of the species is suggested by the presence of troglomorphisms on an advanced degree, especially the reduction of skin pigmentation, the total loss of eyes and the enlarged barbels. In addition, the presence of a well developed adipose fold in adults may indicate a distinctive adaptation acquired by neoteny to withstand the food scarce conditions of its hypogean habitat.