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Korbel KL, Hose GC, Karwautz C, Greenfield P, Wang H, Chariton AA, Griebler C. Detection, movement and persistence of invertebrate eDNA in groundwater. Sci Rep 2024; 14:17151. [PMID: 39060364 PMCID: PMC11282260 DOI: 10.1038/s41598-024-67349-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.
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Affiliation(s)
- K L Korbel
- School of Natural Sciences, Macquarie University, Sydney, Australia.
| | - G C Hose
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - P Greenfield
- Energy Business Unit, Common wealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - H Wang
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Workgroup of Limnology and Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - A A Chariton
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
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.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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Couton M, Studer A, Hürlemann S, Locher N, Knüsel M, Alther R, Altermatt F. Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland. Sci Rep 2023; 13:18097. [PMID: 37872363 PMCID: PMC10593815 DOI: 10.1038/s41598-023-44908-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.
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Affiliation(s)
- Marjorie Couton
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
| | - Angela Studer
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Nadine Locher
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Mara Knüsel
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Roman Alther
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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Manenti R, Galbiati M, Lapadula S, Forlani M, Barzaghi B, Melotto A, Ficetola GF. Behavioural drivers of ecotone exploitation: activity of groundwater animals in spring. Behav Ecol Sociobiol 2023. [DOI: 10.1007/s00265-023-03297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Abstract
Border habitats such as interfaces and ecotones are promising research targets being likely areas of high species richness and genetic and phenotypic diversity. Springs are intriguing habitats exploited by both subterranean and surface species. For subterranean species, springs can provide higher trophic resources but can be risky in terms of predation and UV radiation, while for surface species, springs can be safer but less productive environments. We coupled field surveys and laboratory experiments to understand how predation risk and physical constraints, like light occurrence, affect spring exploitation by both a subterranean (Niphargus thuringius) and a surface crustacean amphipod species (Echinogammarus stammeri). From March to May 2021, we surveyed multiple springs and evaluated the activity (both during day and night) of the amphipods and of their predators. Furthermore, in a subterranean laboratory, we reared 80 N. thuringius and 80 E. stammeri under safe and risky conditions with both constant darkness and diel light variation assessing their activity and survival. Risky conditions were represented by the occurrence of meso-predators alone or coupled with the presence of a top predator. In the field, N. thuringius activity was negatively related to the density of predators, while laboratory experiments revealed a main role played by light treatments and night period. E. stammeri activity in the field was higher close to surface while in laboratory conditions decreased during time. In laboratory conditions, predation risk negatively affected survival of both amphipods. Our findings reveal that physical constraints play a key role in affecting the exploitation of ecotones and can mediate antipredator responses, thus providing selective pressures for the exploitation of border environments.
Significance statement
Understanding environmental pressures acting on ecotones is a key point to verify if new adaptations may occur at the border between two distinct habitats. Using both field and laboratory approaches, we show that, in springs, the behaviour of subterranean invertebrates is affected by surface physical constraints which can mediate the effects of predation risk. Behavioural strategies to avoid predation, such as nocturnal activity, may promote spring ecotone exploitation by groundwater animals, such as amphipod crustaceans.
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Mammola S, Meierhofer MB, Borges PA, Colado R, Culver DC, Deharveng L, Delić T, Di Lorenzo T, Dražina T, Ferreira RL, Fiasca B, Fišer C, Galassi DMP, Garzoli L, Gerovasileiou V, Griebler C, Halse S, Howarth FG, Isaia M, Johnson JS, Komerički A, Martínez A, Milano F, Moldovan OT, Nanni V, Nicolosi G, Niemiller ML, Pallarés S, Pavlek M, Piano E, Pipan T, Sanchez‐Fernandez D, Santangeli A, Schmidt SI, Wynne JJ, Zagmajster M, Zakšek V, Cardoso P. Towards evidence-based conservation of subterranean ecosystems. Biol Rev Camb Philos Soc 2022; 97:1476-1510. [PMID: 35315207 PMCID: PMC9545027 DOI: 10.1111/brv.12851] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 12/18/2022]
Abstract
Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History Luomus (LUOMUS)University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
| | - Paulo A.V. Borges
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
| | - Raquel Colado
- Departament of Ecology and HidrologyUniversity of MurciaMurcia30100Spain
| | - David C. Culver
- Department of Environmental ScienceAmerican University4400 Massachusetts Avenue, N.WWashingtonDC20016U.S.A.
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS UMR 7205, MNHN, UPMC, EPHEMuseum National d'Histoire Naturelle, Sorbonne UniversitéParisFrance
| | - Teo Delić
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Tiziana Di Lorenzo
- Research Institute on Terrestrial Ecosystems (IRET‐CNR), National Research CouncilVia Madonna del Piano 10, 50019 Sesto FiorentinoFlorenceItaly
| | - Tvrtko Dražina
- Division of Zoology, Department of BiologyFaculty of Science, University of ZagrebRooseveltov Trg 6Zagreb10000Croatia
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Rodrigo L. Ferreira
- Center of Studies in Subterranean Biology, Biology Department, Federal University of LavrasCampus universitário s/n, Aquenta SolLavrasMG37200‐900Brazil
| | - Barbara Fiasca
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Diana M. P. Galassi
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Laura Garzoli
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Vasilis Gerovasileiou
- Department of Environment, Faculty of EnvironmentIonian University, M. Minotou‐Giannopoulou strPanagoulaZakynthos29100Greece
- Hellenic Centre for Marine Research (HCMR), Institute of Marine BiologyBiotechnology and Aquaculture (IMBBC)Thalassocosmos, GournesCrete71500Greece
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of LimnologyUniversity of ViennaDjerassiplatz 1Vienna1030Austria
| | - Stuart Halse
- Bennelongia Environmental Consultants5 Bishop StreetJolimontWA6014Australia
| | | | - Marco Isaia
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Joseph S. Johnson
- Department of Biological SciencesOhio University57 Oxbow TrailAthensOH45701U.S.A.
| | - Ana Komerički
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Alejandro Martínez
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Filippo Milano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Oana T. Moldovan
- Emil Racovita Institute of SpeleologyClinicilor 5Cluj‐Napoca400006Romania
- Romanian Institute of Science and TechnologySaturn 24‐26Cluj‐Napoca400504Romania
| | - Veronica Nanni
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Giuseppe Nicolosi
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Matthew L. Niemiller
- Department of Biological SciencesThe University of Alabama in Huntsville301 Sparkman Drive NWHuntsvilleAL35899U.S.A.
| | - Susana Pallarés
- Departamento de Biogeografía y Cambio GlobalMuseo Nacional de Ciencias Naturales, CSICCalle de José Gutiérrez Abascal 2Madrid28006Spain
| | - Martina Pavlek
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
- Ruđer Bošković InstituteBijenička cesta 54Zagreb10000Croatia
| | - Elena Piano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Tanja Pipan
- ZRC SAZUKarst Research InstituteNovi trg 2Ljubljana1000Slovenia
- UNESCO Chair on Karst EducationUniversity of Nova GoricaGlavni trg 8Vipava5271Slovenia
| | | | - Andrea Santangeli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiViikinkaari 1Helsinki00014Finland
| | - Susanne I. Schmidt
- Institute of Hydrobiology, Biology Centre CASNa Sádkách 702/7České Budějovice370 05Czech Republic
- Department of Lake ResearchHelmholtz Centre for Environmental ResearchBrückstraße 3aMagdeburg39114Germany
| | - J. Judson Wynne
- Department of Biological SciencesCenter for Adaptable Western Landscapes, Box 5640, Northern Arizona UniversityFlagstaffAZ86011U.S.A.
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
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Kennedy MD, Connaughton VP. Differential effects of fluoxetine on the phototactic behavior of 3 amphipod species (Crustacea; Amphipoda). ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 93:103889. [PMID: 35605929 DOI: 10.1016/j.etap.2022.103889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
We document phototactic responses in different amphipod populations of Gammarus minus, Stygobromus tenuis, and Crangonyx shoemakeri, each collected at 2-3 sites within the Washington DC area. We then assessed how baseline phototaxis was altered following either short-term (3-week) or long-term (6-week) exposure to 0.05 µg/L or 0.5 µg/L fluoxetine. Our results classify all species as significantly photonegative, a response that depended solely on the presence, not quality, of light. Short-term fluoxetine exposure caused some animals to become photoneutral, regardless of concentration, while others remained photonegative. Long-term exposure to 0.5 µg/L fluoxetine caused photoneutral behaviors in all surviving populations; exposure to 0.05 µg/L had variable effects. These differential effects were due to a significant effect of population/sampling location on photobehavior. Overall, these results identify species-specific effects of chronic fluoxetine exposure and underscore how the response to light in 7 geographically distinct populations is uniquely tuned to requirements for survival.
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Ray M, Umapathy G. Environmental DNA as a tool for biodiversity monitoring in aquatic ecosystems – a review. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.7837.14.5.21102-21116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The monitoring of changes in aquatic ecosystems due to anthropogenic activities is of utmost importance to ensure the health of aquatic biodiversity. Eutrophication in water bodies due to anthropogenic disturbances serves as one of the major sources of nutrient efflux and consequently changes the biological productivity and community structure of these ecosystems. Habitat destruction and overexploitation of natural resources are other sources that impact the equilibrium of aquatic systems. Environmental DNA (eDNA) is a tool that can help to assess and monitor aquatic biodiversity. There has been a considerable outpour of research in this area in the recent past, particularly concerning conservation and biodiversity management. This review focuses on the application of eDNA for the detection and relative quantification of threatened, endangered, invasive and elusive species. We give a special emphasis on how this technique developed in the past few years to become a tool for understanding the impact of spatial-temporal changes on ecosystems. Incorporating eDNA based biomonitoring with advances in sequencing technologies and computational abilities had an immense role in the development of different avenues of application of this tool.
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Dooley KE, Niemiller KDK, Sturm N, Niemiller ML. Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.43.79993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Shelta Cave Crayfish (Orconectes sheltae) is a small, cave-obligate member of the genus Orconectes (family Cambaridae) endemic to a single cave system—Shelta Cave—in northwest Huntsville, Madison Co., Alabama, USA. Although never abundant, this stygobiont was regularly observed in the 1960s and early 1970s before the population and aquatic community in general at Shelta Cave collapsed likely in response to groundwater contamination and the loss of energetic inputs from a Grey Bat (Myotis grisescens) maternity colony that abandoned the cave after installation of a poorly designed cave gate. We conducted 20 visual surveys of aquatic habitats at Shelta Cave between October 2018 and July 2021. Although the aquatic community has not recovered, we did confirm the continued existence of O. sheltae, which had not been observed in 31 years, with observations of an adult female on 31 May 2019 and an adult male on 28 August 2020. We conducted the first phylogenetic analyses of O. sheltae and discovered that the species is most closely related to other geographically proximate stygobiotic crayfishes in the genus Cambarus in northern Alabama than members of the genus Orconectes. We advocate for recognition of this species as Cambarus sheltae to more accurately reflect evolutionary relationships of this single-cave endemic and offer recommendations for its management, conservation, and future research, as this species remains at high risk of extinction.
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
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.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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10
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Weigand A, Bücs SL, Deleva S, Lukić Bilela L, Nyssen P, Paragamian K, Ssymank A, Weigand H, Zakšek V, Zagmajster M, Balázs G, Barjadze S, Bürger K, Burn W, Cailhol D, Decrolière A, Didonna F, Doli A, Drazina T, Dreybrodt J, Ðud L, Egri C, Erhard M, Finžgar S, Fröhlich D, Gartrell G, Gazaryan S, Georges M, Godeau JF, Grunewald R, Gunn J, Hajenga J, Hofmann P, Knight L, Köble H, Kuharic N, Lüthi C, Munteanu C, Novak R, Ozols D, Petkovic M, Stoch F, Vogel B, Vukovic I, Hall Weberg M, Zaenker C, Zaenker S, Feit U, Thies JC. Current cave monitoring practices, their variation and recommendations for future improvement in Europe: A synopsis from the 6th EuroSpeleo Protection Symposium. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e85859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted.
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11
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Moss WE, Harper LR, Davis MA, Goldberg CS, Smith MM, Johnson PTJ. Navigating the trade‐offs between environmental
DNA
and conventional field surveys for improved amphibian monitoring. Ecosphere 2022. [DOI: 10.1002/ecs2.3941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wynne E. Moss
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Lynsey R. Harper
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
- NatureMetrics Ltd, CABI Site Egham UK
| | - Mark A. Davis
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
| | - Caren S. Goldberg
- School of the Environment Washington State University Pullman Washington USA
| | - Matthew M. Smith
- School of the Environment Washington State University Pullman Washington USA
| | - Pieter T. J. Johnson
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
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12
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van den Berg-Stein S, Hahn HJ, Thielsch A, Schwenk K. Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes. WATER RESEARCH 2022; 210:117956. [PMID: 35032894 DOI: 10.1016/j.watres.2021.117956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Groundwater is one of our most important resources, however groundwater ecosystems are among the most understudied habitats of the planet earth. Studies on groundwater organisms are hampered by the difficult accessibility of species, the lack of morphological differentiation and the limitation for laboratory cultures. One important approach to overcome these shortcomings is to provide sensitive genetic methods to unravel patterns of biodiversity, population structure and gene flow in natural populations. In this study we present five sets of microsatellite markers developed for the isopods Asellus aquaticus and Proasellus slavus, the cyclopoides Paracyclops fimbriatus and Acanthocyclops sensitivus and the harpacticoide Bryocamptus echinatus (Crustacea). Two of these species were subjected to detailed population genetic analyses: We studied 501 specimens of Asellus aquaticus from four different regions in Northern Germany using nine microsatellite markers and 70 specimens of Bryocamptus echinatus using nine microsatellite markers from three different sampling sites in South-Western Germany. Our results show that genetic diversity is high (A. aquaticus: 10 to 20 and B. echinatus: 4 to 18 alleles per locus) among populations of aquatic invertebrates, populations are highly differentiated (FST > 0.2) and genetic differentiation was associated with geographic patterns. Applications of molecular genetic methods and their use for the detection of hydrological exchange processes relevant for drinking water suppliers are demonstrated and discussed.
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Affiliation(s)
- Susanne van den Berg-Stein
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany; Institute for Groundwater Ecology IGÖ GmbH, University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany.
| | - Hans Jürgen Hahn
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany; Institute for Groundwater Ecology IGÖ GmbH, University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
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13
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Gladstone NS, Niemiller ML, Hutchins B, Schwartz B, Czaja A, Slay ME, Whelan NV. Subterranean freshwater gastropod biodiversity and conservation in the United States and Mexico. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13722. [PMID: 33598995 DOI: 10.1111/cobi.13722] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/06/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Many taxonomic groups successfully exploit groundwater environments and have adapted to a subterranean (stygobiotic) existence. Among these groups are freshwater gastropods (stygosnails), which represent a widespread and taxonomically diverse component of groundwater ecosystems in North America. However, owing to sampling difficulty and lack of targeted study, stygosnails remain among the most understudied of all subterranean groups. We conducted a literature review to assess the biodiversity and geographic associations of stygosnails, along with the threats, management activities, and policy considerations related to the groundwater systems they inhabit. We identified 39 stygosnail species known to occur in a range of groundwater habitats from karst regions in the United States and Mexico. Most stygosnails exhibit extreme narrow-range endemism, resulting in a high risk of extinction from a single catastrophic event. We found that anthropogenically driven changes to surface environments have led to changes in local hydrology and degradation of groundwater systems inhabited by stygosnails such as increased sedimentation, introduction of invasive species, groundwater extraction, or physical collapse of water-bearing passages. Consequently, 32 of the 39 described stygosnail species in the United States and Mexico have been assessed as imperiled under NatureServe criteria, and 10 species have been assessed as threatened under International Union for Conservation of Nature criteria. Compared with surface species of freshwater snails, stygosnail conservation is uniquely hindered by difficulties associated with accessing subterranean habitats for monitoring and management. Furthermore, only three species were found to have federal protection in either the United States or Mexico, and current laws regulating wildlife and water pollution at the state and federal level may be inadequate for protecting stygosnail habitats. As groundwater systems continue to be manipulated and relied on by humans, groundwater-restricted fauna such as stygosnails should be studied so unique biodiversity can be protected.
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Affiliation(s)
- Nicholas S Gladstone
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, Alabama, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Benjamin Hutchins
- Edwards Aquifer Research and Data Center, Texas State University, San Marcos, Texas, USA
| | - Benjamin Schwartz
- Edwards Aquifer Research and Data Center, Texas State University, San Marcos, Texas, USA
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Alexander Czaja
- Faculty of Biological Sciences, Juárez University of the State of Durango, Gómez Palacio, Mexico
| | - Michael E Slay
- Arkansas Field Office, The Nature Conservancy, Little Rock, Arkansas, USA
| | - Nathan V Whelan
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, Alabama, USA
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, Alabama, USA
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14
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Premate E, Zagmajster M, Fišer C. Inferring predator-prey interaction in the subterranean environment: a case study from Dinaric caves. Sci Rep 2021; 11:21682. [PMID: 34737417 PMCID: PMC8568937 DOI: 10.1038/s41598-021-01249-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Predator–prey interactions are among the most important biotic interactions shaping ecological communities and driving the evolution of defensive traits. These interactions and their effects on species received little attention in extreme and remote environments, where possibilities for direct observations and experimental manipulation of the animals are limited. In this paper, we study such type of environment, namely caves of the Dinarides (Europe), combining spatial and phylogenetic methods. We focused on several species of Niphargus amphipods living in phreatic lakes, as some of them use the dorsal spines as putative morphological defensive traits. We predicted that these spines represent a defense strategy against the olm (Proteus anguinus), a top predator species in the subterranean waters. We tested for spatial overlap of the olm and Niphargus species and showed that spined species live in closer proximity to and co-occur more frequently with the olm than non-spined species. Modeling of the evolution of the spines onto Niphargus phylogeny implies coevolution of this trait in the presence of olm. We conclude that these spines likely evolved as defensive traits in a predator–prey arms race. Combining multiple analyses, we provide an example for a methodological framework to assess predator–prey interactions when in-situ or laboratory observations are not possible.
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Affiliation(s)
- Ester Premate
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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15
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Species status evaluation of Lirceus usdagalan, L. culveri, and L. hargeri populations (Isopoda; Asellidae) based on a large scale next-generation sequence data set. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01387-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Postojna-Planina Cave System in Slovenia, a Hotspot of Subterranean Biodiversity and a Cradle of Speleobiology. DIVERSITY 2021. [DOI: 10.3390/d13060271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and join underground into Unica River, which emerges to the surface. The studies of fauna of PPCS began in the 19th century with the first scientific descriptions of specialized cave animals in the world, making it “the cradle of speleobiology”. Currently, the species list of PPCS contains 116 troglobiotic animal species belonging to eight phyla, confirming its status as the richest in the world. Of these, 47 species have been scientifically described from the PPCS, and more than 10 await formal taxonomic descriptions. We expect that further sampling, detailed analyses of less studied taxa, and the use of molecular methods may reveal more species. To keep the cave animals’ checklist in PPCS up-to-date, we have supplemented the printed checklist with an online interface. As the revised checklist is a necessary first step for further activities, we discuss the importance of PPCS in terms of future research and conservation.
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17
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Mouser JB, Brewer SK, Niemiller ML, Mollenhauer R, Van Den Bussche RA. Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.39.64279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.
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18
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Mammola S, Lunghi E, Bilandžija H, Cardoso P, Grimm V, Schmidt SI, Hesselberg T, Martínez A. Collecting eco-evolutionary data in the dark: Impediments to subterranean research and how to overcome them. Ecol Evol 2021; 11:5911-5926. [PMID: 34141192 PMCID: PMC8207145 DOI: 10.1002/ece3.7556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022] Open
Abstract
Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so-called "cave species." Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.Our over-arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS)University of HelsinkiHelsinkiFinland
- Dark‐MEG: Molecular Ecology GroupWater Research Institute (IRSA)National Research Council (CNR)VerbaniaItaly
| | - Enrico Lunghi
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Museo di Storia Naturale dell'Università degli Studi di Firenze“La Specola”FirenzeItaly
| | - Helena Bilandžija
- Department of Molecular BiologyRudjer Boskovic InstituteZagrebCroatia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS)University of HelsinkiHelsinkiFinland
| | - Volker Grimm
- Department of Ecological ModellingHelmholtz Centre for Environmental Research – UFZLeipzigGermany
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Susanne I. Schmidt
- Institute of HydrobiologyBiology Centre CASČeské BudějoviceCzech Republic
| | | | - Alejandro Martínez
- Dark‐MEG: Molecular Ecology GroupWater Research Institute (IRSA)National Research Council (CNR)VerbaniaItaly
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19
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Benito JB, Porter ML, Niemiller ML. The mitochondrial genomes of five spring and groundwater amphipods of the family Crangonyctidae (Crustacea: Amphipoda) from eastern North America. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1662-1667. [PMID: 34104729 PMCID: PMC8143621 DOI: 10.1080/23802359.2021.1926350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We sequenced the mitochondrial genomes of one spring-dwelling (Crangonyx forbesi) and four groundwater amphipods (Bactrurus brachycaudus, Stygobromus allegheniensis, S. pizzinii, and S. t. potomacus) from eastern North America using a shotgun sequencing approach on an Illumina HiSeq 4000 (Illumina, San Diego, CA). All five mitochondrial genomes encoded 13 protein-coding genes, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs) representative of subphylum Crustacea. Although the four groundwater species exhibited gene orders nearly identical to the ancestral pancrustacean gene order, the spring-dwelling species, C. forbesi, possessed a transposition of the trnH–nad4–nad4l loci downstream after nad6–cytb–trnS2. Moreover, a long nad5 locus, longer rrnL, and rrnS loci, and unconventional start codons distinguished C. forbesi from the four groundwater amphipods. Overall, our five amphipod mitogenomes add to the increasing publicly available mitogenome resources for amphipods that are not only valuable for studying the evolutionary relationships of this diverse group of crustaceans but for exploring the evolution of mitochondrial genomes in general.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
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20
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Gibson R, Hutchins BT, Krejca JK, Diaz PH, Sprouse PS. Stygobromus bakeri, a new species of groundwater amphipod (Amphipoda, Crangonyctidae) associated with the Trinity and Edwards aquifers of central Texas, USA. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.38.61787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new stygobitic groundwater amphipod species, Stygobromus bakerisp. nov., is described from 4 central Texas limestone karst springs; John Knox Spring (Comal County), Jacob’s Well (Hays County), Mormon Spring (Travis County) and Salado Springs (Bell County). This species belongs to the predominately western Nearctic hubbsi species group of Stygobromus and differs from other species in the group by gnathopod 1 with row of 4 to 5 setae posterior to the defining angle, pereopods 6 and 7 with broadly expanded bases and distinct distoposterior lobes, gnathopods 1 and 2 with 2 rows of 3 singly inserted setae on the inner palm, and uropod 3 with single, slightly distal peduncular seta. Habitat, sympatric groundwater species, and conservation issues are discussed.
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21
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Tarof SA, Crookes S, Moxley K, Hathaway J, Cameron G, Hanner RH. Environmental DNA bioassays corroborate field data for detection of overwintering species at risk Blanding's turtles ( Emydoidea blandingii). Genome 2021; 64:299-310. [PMID: 33538216 DOI: 10.1139/gen-2020-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Environmental DNA (eDNA) is gaining traction in conservation ecology as a powerful tool for detecting species at risk. We developed a quantitative polymerase chain reaction assay to detect a DNA amplicon fragment of the mitochondrial nicotinamide adenine dinucleotide locus of the Blanding's turtle (Emydoidea blandingii) for detecting overwintering individuals. Seventy-eight water samples were collected from 17 wetland sites in Ontario, Canada. We used traditional field data to identify a priori positive and negative control sites. Fifty percent of positive control sites amplified. Detection was related to the number of individuals estimated from field observations in at least one region surveyed. Positive control sites had lower total dissolved solids and electrical conductivity in relation to negative control sites. Shedding rates were within the same order of magnitude for brumating and active turtles. We recommend collecting additional samples at a larger number of locations to maximize detection. Recommended sampling design changes may overshadow the additional effects of water chemistry and low eDNA shedding rates. eDNA offers tremendous potential to practitioners conducting species at risk assessments in environmental consulting by providing a faster, more efficient method of detection compared with traditional surveys.
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Affiliation(s)
- Scott A Tarof
- Azimuth Environmental Consulting, Inc., 642 Welham Road, Barrie, ON L4N 9A1, Canada
| | - Steven Crookes
- Precision Biomonitoring Inc., Orchard Park, Suite #226, 5420 Highway 6 North, Guelph, ON N1H 6J2, Canada
| | - Kelsey Moxley
- Scales Nature Park, 82 Line 15 South, Oro-Medonte, ON L3V 8H9, Canada
| | - Jeff Hathaway
- Scales Nature Park, 82 Line 15 South, Oro-Medonte, ON L3V 8H9, Canada
| | - Graham Cameron
- Ministry of Natural Resources and Forestry (Bancroft District), 106 Monck Street, Bancroft, ON K0L 1C0, Canada
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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22
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Troth CR, Burian A, Mauvisseau Q, Bulling M, Nightingale J, Mauvisseau C, Sweet MJ. Development and application of eDNA-based tools for the conservation of white-clawed crayfish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141394. [PMID: 32814295 DOI: 10.1016/j.scitotenv.2020.141394] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/20/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
eDNA-based methods represent non-invasive and cost-effective approaches for species monitoring and their application as a conservation tool has rapidly increased within the last decade. Currently, they are primarily used to determine the presence/absence of invasive, endangered or commercially important species, but they also hold potential to contribute to an improved understanding of the ecological interactions that drive species distributions. However, this next step of eDNA-based applications requires a thorough method development. We developed an eDNA assay for the white-clawed crayfish (Austropotamobius pallipes), a flagship species of conservation in the UK and Western Europe. Multiple subsequent in-situ and ex-situ validation tests aimed at improving method performance allowed us to apply eDNA-based surveys to evaluate interactions between white-clawed crayfish, crayfish plague and invasive signal crayfish. The assay performed well in terms of specificity (no detection of non-target DNA) and sensitivity, which was higher compared to traditional methods (in this case torching). The eDNA-based quantification of species biomass was, however, less reliable. Comparison of eDNA sampling methods (precipitation vs. various filtration approaches) revealed that optimal sampling method differed across environments and might depend on inhibitor concentrations. Finally, we applied our methodology together with established assays for crayfish plague and the invasive signal crayfish, demonstrating their significant interactions in a UK river system. Our analysis highlights the importance of thorough methodological development of eDNA-based assays. Only a critical evaluation of methodological strengths and weaknesses will allow us to capitalise on the full potential of eDNA-based methods and use them as decision support tools in environmental monitoring and conservation practice.
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Affiliation(s)
- Christopher R Troth
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; SureScreen Scientifics Ltd, Morley Retreat, Church Lane, Morley DE7 6DE, UK.
| | - Alfred Burian
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Quentin Mauvisseau
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; SureScreen Scientifics Ltd, Morley Retreat, Church Lane, Morley DE7 6DE, UK
| | - Mark Bulling
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Jen Nightingale
- Bristol Zoological Society, Clifton, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK
| | - Christophe Mauvisseau
- Fédération de Pêche et de Protection du Milieu Aquatique du Loir-et-Cher, 11 Rue Robert Nau, 41000 Blois, France
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK.
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23
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Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama. PLoS One 2020; 15:e0242741. [PMID: 33301442 PMCID: PMC7728221 DOI: 10.1371/journal.pone.0242741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022] Open
Abstract
The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatened, and endangered taxa. However, there are few eDNA studies of groundwater fauna. Here we report the results of the development and implementation of an eDNA assay targeting a short fragment of the mitochondrial CO1 locus of a critically imperiled cave crayfish, the Sweet Home Alabama Cave Crayfish (Cambarus speleocoopi), known from just four cave systems in the Interior Plateau karst region of northern Alabama. We detected C. speleocoopi DNA from water samples collected at 5 of 16 sites sampled (caves and springs), including two historical sites as well as three additional and potentially new sites in Marshall County, Alabama. All three of these sites were within 2 km of historical sites. Our study is the first to detect a groundwater crustacean in the Interior Plateau karst region. Additionally, our study contributes to the growing literature that eDNA is a viable complementary tool for detection and monitoring of a fauna that is difficult to survey and study using traditional approaches.
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Mammola S, Amorim IR, Bichuette ME, Borges PAV, Cheeptham N, Cooper SJB, Culver DC, Deharveng L, Eme D, Ferreira RL, Fišer C, Fišer Ž, Fong DW, Griebler C, Jeffery WR, Jugovic J, Kowalko JE, Lilley TM, Malard F, Manenti R, Martínez A, Meierhofer MB, Niemiller ML, Northup DE, Pellegrini TG, Pipan T, Protas M, Reboleira ASPS, Venarsky MP, Wynne JJ, Zagmajster M, Cardoso P. Fundamental research questions in subterranean biology. Biol Rev Camb Philos Soc 2020; 95:1855-1872. [DOI: 10.1111/brv.12642] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Isabel R. Amorim
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Maria E. Bichuette
- Laboratory of Subterranean Studies Federal University of São Carlos Rodovia Washington Luís km 235 São Carlos São Paulo 13565‐905 Brazil
| | - Paulo A. V. Borges
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science Thompson Rivers University 805 TRU Way Kamloops British Columbia Canada
| | - Steven J. B. Cooper
- Evolutionary Biology Unit South Australian Museum North Terrace Adelaide South Australia 5000 Australia
- Australian Centre for Evolutionary Biology and Biodiversity, and Environment Institute, School of Biological Sciences University of Adelaide Adelaide South Australia 5005 Australia
| | - David C. Culver
- Department of Environmental Science American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Louis Deharveng
- UMR7205 – ISYEB Museum national d'Histoire naturelle 45 rue Buffon (CP50) Paris 75005 France
| | - David Eme
- IFREMER Centre Atlantique Unité Ecologie et Modèles pour l'Halieutique Rue de l'Île d'Yeu Nantes 44980 France
| | - Rodrigo Lopes Ferreira
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Žiga Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Daniel W. Fong
- Department of Biology American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of Limnology University of Vienna Althanstrasse 14 Vienna 1090 Austria
| | - William R. Jeffery
- Department of Biology University of Maryland College Park MD 20742 U.S.A
| | - Jure Jugovic
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies University of Primorska Glagoljaška 8 Koper SI‐6000 Slovenia
| | - Johanna E. Kowalko
- Harriet L. Wilkes Honors College Florida Atlantic University 5353 Parkside Dr Jupiter FL 33458 U.S.A
| | - Thomas M. Lilley
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
| | - Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1, ENTPE, CNRS, Université de Lyon, Bat. Forel 6 rue Raphaël Dubois Villeurbanne cedex 69622 France
| | - Raoul Manenti
- Department of Environmental Science and Policy Università degli Studi di Milano Via Celoria 26 Milan 20113 Italy
| | - Alejandro Martínez
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Department of Rangeland, Wildlife and Fisheries Management Texas A&M University 534 John Kimbrough Blvd. College Station TX 77843 U.S.A
| | - Matthew L. Niemiller
- Department of Biological Sciences The University of Alabama in Huntsville 301 Sparkman Drive NW Huntsville AL 35899 U.S.A
| | - Diana E. Northup
- Department of Biology University of New Mexico Albuquerque NM 87131‐0001 U.S.A
| | - Thais G. Pellegrini
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Tanja Pipan
- ZRC SAZU Karst Research Institute Novi trg 2 Ljubljana SI‐1000 Slovenia
- UNESCO Chair on Karst Education University of Nova Gorica Vipavska cesta Nova Gorica 5000 Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics Domenicas University of California 50 Acacia Avenue San Rafael CA 94901 U.S.A
| | - Ana Sofia P. S. Reboleira
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen 2100 Denmark
| | - Michael P. Venarsky
- Australian Rivers Institute Griffith University 170 Kessels Road Nathan Queensland 4111 Australia
| | - J. Judson Wynne
- Department of Biological Sciences, Center for Adaptable Western Landscapes Northern Arizona University Box 5640 Flagstaff AZ 86011 U.S.A
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
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Habitats and Diversity of Subterranean Macroscopic Freshwater Invertebrates: Main Gaps and Future Trends. WATER 2020. [DOI: 10.3390/w12082170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Caves are the best studied aquatic subterranean habitat, but there is a wide variety of these habitats, ranging in depth below the surface and size of the spaces (pore or habitat size). Both factors are important in setting limits to species composition and richness. In addition to caves, among the most important shallow aquatic subterranean habitats are the hyporheal (underflow of rivers and streams), the hypotelminorheal (very superficial drainages with water exiting in seeps), epikarst, and calcrete aquifers. Although it is little studied, both body size and species composition in the different habitats is different. Because of high levels of endemism and difficulty in access, no subterranean habitats are well sampled, even caves. However, there are enough data for robust generalizations about some geographic patterns. Individual hotspot caves are concentrated in the Dinaric region of southern Europe, and overall, tropical regions have fewer obligate aquatic cave dwellers (stygobionts). In all subterranean aquatic habitats, regional diversity is much higher than local diversity, but local diversity (especially single cave diversity) may be a useful predictor of regional species richness. In Europe there is a ridge of high aquatic subterranean species richness basically extending east from the French–Spanish border. Its cause may be either high productivity or that long-term temperature oscillations are at a minimum. With increased collecting and analysis, global and continental trends should become clearer.
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Gibson L, Humphreys WF, Harvey M, Hyder B, Winzer A. Shedding light on the hidden world of subterranean fauna: A transdisciplinary research approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:381-389. [PMID: 31154211 DOI: 10.1016/j.scitotenv.2019.05.316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/18/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
Subterranean environments contain a diverse and unique obligate fauna: either aquatic living in the groundwater or terrestrial living in voids above the water table. In the arid region of the western part of the Australian continent, a particularly rich subterranean fauna coincides with a concentration of natural resource extraction operations. Since the inclusion of subterranean fauna in assessments of environmental impact in the mid-1990s, taxonomic research in Australia on this group of mainly invertebrates has grown exponentially. However, remaining knowledge gaps continue to frustrate both environmental regulators and development proponents due to high uncertainty in the decision-making process. In early 2017, the Western Australian Biodiversity Science Institute was tasked with leading the development of a research program to improve on the current state of knowledge of subterranean fauna. To balance the diverse environmental, economic and social needs of a range of stakeholders, transdisciplinary principles were applied to program development. A clear consensus on five broad focus areas to progress include: (1) data consolidation; (2) resilience to disturbance; (3) survey and sampling protocols; (4) abiotic and biotic habitat requirements; and (5) species delineation. In the context of these focus areas; we describe the research program development, reviewing the status of knowledge within each focus area, and the research initiatives to close the gaps in knowledge. We argue that, by adopting a transdisciplinary approach, the likelihood of success of the research program, as measured by the effective translation and adoption of research findings, will be maximized. This review is timely given the ever-increasing demand on groundwater systems for water extraction worldwide. A holistic understanding of the influence of anthropogenic activities on these ecosystems, and the functional role of organisms within them, will help to ensure that their health is not compromised.
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Affiliation(s)
- Lesley Gibson
- Western Australian Biodiversity Science Institute, WA Trustees Building, Level 2, 133 St Georges Terrace, Perth, WA 6000, Australia; Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA 6151, Australia; School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - William F Humphreys
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - Mark Harvey
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - Bridget Hyder
- Department of Water and Environmental Regulation, 8 Davidson Terrace, Joondalup, Western Australia 6027, Australia
| | - Andrew Winzer
- Fortescue Metals Group Ltd, Level 2, 87 Adelaide Terrace, East Perth, Western Australia 6004, Australia
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27
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Saccò M, Blyth A, Bateman PW, Hua Q, Mazumder D, White N, Humphreys WF, Laini A, Griebler C, Grice K. New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:963-977. [PMID: 30795483 DOI: 10.1016/j.scitotenv.2019.01.296] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (14C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ13C) and nitrogen (δ15N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, 14C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and 14C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.
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Affiliation(s)
- Mattia Saccò
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia.
| | - Alison Blyth
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Philip W Bateman
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Nicole White
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - William F Humphreys
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6986, Australia; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Alex Laini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale G.P. Usberti 33/A, 43124 Parma, Italy
| | - Christian Griebler
- Helmholtz Center Munich, Institute of Groundwater Ecology, Neuherberg, Germany; University of Vienna, Dept of Limnology and Bio-Oceanography, Vienna, Austria
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
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28
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Copilaş-Ciocianu D, Sidorov D, Gontcharov A. Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipods. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00401-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Sellers GS, Di Muri C, Gómez A, Hänfling B. Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.24556] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Efficient DNA extraction is fundamental to molecular studies. However, commercial kits are expensive when a large number of samples need to be processed. Here we present a simple, modular and adaptable DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types (modular universal DNA extraction method or Mu-DNA). We compare the performance of our method to that of widely used commercial kits across a range of soil, stool, tissue and water samples. Mu-DNA produced DNA extractions of similar or higher yield and purity to that of the commercial kits. As a proof of principle, we carried out replicate fish metabarcoding of aquatic eDNA extractions, which confirmed that the species detection efficiency of our method is similar to that of the most frequently used commercial kit. Our results demonstrate the reliability of Mu-DNA along with its modular adaptability to challenging sample types and sample collection methods. Mu-DNA can substantially reduce the costs and increase the scope of experiments in molecular studies.
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