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Macher TH, Arle J, Beermann AJ, Frank L, Hupało K, Koschorreck J, Schütz R, Leese F. Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream. PeerJ 2024; 12:e18016. [PMID: 39465159 PMCID: PMC11512801 DOI: 10.7717/peerj.18016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 10/29/2024] Open
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, a limitation of eDNA surveys is that detected DNA molecules may originate from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding has recently been proposed as a complementary tool for more localized assessments of the biological community. In this study, we evaluated the effectiveness of eDNA and eRNA metabarcoding for inferring the richness and species distribution patterns of vertebrates and invertebrates in a Central European lowland river. We collected water samples and analyzed them using a 12S marker for vertebrates and a COI marker for invertebrates. We detected 31 fish, 16 mammal, 10 bird and one lamprey species in the vertebrate dataset. While results were largely consistent, we detected a higher number of species when analysing eRNA (mean = 30.89) than eDNA (mean = 26.16). Also, eRNA detections had a stronger local signature than eDNA detections when compared against species distribution patterns from traditional fish monitoring data. For invertebrates, we detected 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan and four cnidarian species. In contrast to the pattern of vertebrate richness, we detected a higher richness using eDNA (mean = 41.37) compared to eRNA (mean = 22.42). Our findings primarily show that eDNA and eRNA-based detections are comparable for vertebrate and invertebrate taxa. Biological replication was important for both template molecules studied. Signal detections for vertebrates were more localized for eRNA compared to eDNA. Overall, the advantages of the extra steps needed for eRNA analyses depend on the study question but both methods provide important data for biodiversity monitoring and research.
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Affiliation(s)
- Till-Hendrik Macher
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
- Biogeography, University of Trier, Trier, Germany
| | - Jens Arle
- German Environment Agency, Berlin, Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Lina Frank
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Kamil Hupało
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | | | - Robin Schütz
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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2
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Lei B, Wang X, Wang L, Kang Y, Wan T, Li W, Yang Q, Zhang J. Combining chemical analysis and toxicological methods to access the ecological risk of complex contamination in Daye Lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173690. [PMID: 38825198 DOI: 10.1016/j.scitotenv.2024.173690] [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: 11/23/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
As one of the nine primary non-ferrous metal smelting bases in China, Daye Lake basin was polluted due to diverse human activities. But so far the pollution status and related ecological risks of this region have not been detailly investigated. In current study, pollutants including heavy metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in eight sediment samples from Daye Lake were quantified. 18S rRNA gene sequencing was employed to profile the nematode community structure within these sediments. Model organism Caenorhabditis elegans (C. elegans) were further applied for a comprehensive ecological risk assessment of Daye Lake. Notably, Cadmium (Cd) was identified as a key driver of ecological risk, reaching an index of 1287.35. At sample point S4, OCPs particularly p,p'-DDT, displayed an extreme ecological risk with a value of 23.19. Cephalobidae and Mononchida showed strong sensitivity to pollutant levels, reinforcing their suitability as robust bioindicators. The composite pollutants in sampled sediments caused oxidative stress in C. elegans, with gene Vit-2 and Mtl-1 as sensitive biomarkers. By employing the multiple analysis methods, our data can offer valuable contributions to environmental monitoring and health risk assessment for composite polluted areas.
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Affiliation(s)
- Bo Lei
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Yue Kang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Tianying Wan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjuan Li
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Qingqing Yang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Jie Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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Kamberović J, Gligora Udovič M, Kulaš A, Tapolczai K, Orlić S, Jusufović A, Gajić A, Žutinić P, Ahmić A, Kalamujić Stroil B. The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina). Microorganisms 2024; 12:1722. [PMID: 39203564 PMCID: PMC11357282 DOI: 10.3390/microorganisms12081722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/13/2024] [Accepted: 08/18/2024] [Indexed: 09/03/2024] Open
Abstract
Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.
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Affiliation(s)
- Jasmina Kamberović
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | - Marija Gligora Udovič
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Antonija Kulaš
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Kálmán Tapolczai
- HUN-REN Balaton Limnological Research Institute, H-8237 Tihany, Hungary
| | - Sandi Orlić
- Institute Ruđer Bošković, HR-10000 Zagreb, Croatia
| | - Amela Jusufović
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | | | - Petar Žutinić
- Department of Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia; (M.G.U.); (A.K.); (P.Ž.)
| | - Adisa Ahmić
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, BA-75000 Tuzla, Bosnia and Herzegovina; (J.K.)
| | - Belma Kalamujić Stroil
- Society for Genetic Conservation of B&H Endemic and Autochthonous Resources, BA-71000 Sarajevo, Bosnia and Herzegovina;
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, BA-71000 Sarajevo, Bosnia and Herzegovina
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Cook LSJ, Briscoe AG, Fonseca VG, Boenigk J, Woodward G, Bass D. Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. Trends Microbiol 2024:S0966-842X(24)00173-2. [PMID: 39164135 DOI: 10.1016/j.tim.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024]
Abstract
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
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Affiliation(s)
- Lauren S J Cook
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Andrew G Briscoe
- Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; NatureMetrics, Surrey Research Park, Guildford GU2 7HJ, UK
| | - Vera G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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Kim YS, Yun HS, Lee JH, Lee KL, Choi JS, Won DH, Kim YJ, Kim HS, Yoon HS. Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula. MICROBIAL ECOLOGY 2024; 87:95. [PMID: 39017940 PMCID: PMC11255046 DOI: 10.1007/s00248-024-02396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 07/18/2024]
Abstract
The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.
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Affiliation(s)
- Young-Saeng Kim
- Research Institute of Ulleung-do & Dok-do, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyun-Sik Yun
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Hak Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Lak Lee
- Water Environmental Engineering Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jae-Sin Choi
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Doo Hee Won
- Doohee Institute of Ecological Research, Korea Ecosystem Service Inc., Ansan, 15426, Republic of Korea
| | - Yong Jae Kim
- Department of Biomedical Science, Daejin University, Pocheon, 11159, Republic of Korea
| | - Han-Soon Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Research Institute of Ulleung-do & Dok-do, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ho-Sung Yoon
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Lu Q, Zhang SY, Du J, Liu Q, Dong C, Zhao J, Wang Y, Yao M. Multi-group biodiversity distributions and drivers of metacommunity organization along a glacial-fluvial-limnic pathway on the Tibetan plateau. ENVIRONMENTAL RESEARCH 2023; 220:115236. [PMID: 36621545 DOI: 10.1016/j.envres.2023.115236] [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: 11/15/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extensive global glacial retreats are threatening cryosphere ecosystem functioning and the associated biota in glacier-fed water systems. Understanding multi-group biodiversity distributions and compositional variation across diverse but hydrologically linked habitats under varying glacial influences will help explain the mechanisms underlying glacial community organization and ecosystem processes. However, such data are generally lacking due to the difficulty of obtaining biodiversity information across wide taxonomic ranges. Here, we used a multi-marker environmental DNA metabarcoding approach to simultaneously investigate the spatial patterns of community compositions and assembly mechanisms of four taxonomic groups (cyanobacteria, diatoms, invertebrates, and vertebrates) along the flowpaths of a tributary of Lake Nam Co on the Tibetan Plateau-from its glacier headwaters, through its downstream river and wetlands, to its estuary. We detected 869 operational taxonomic units: 119 cyanobacterial, 395 diatom, 269 invertebrate, and 86 vertebrate. Taxonomic richnesses consistently increased from upstream to downstream, and although all groups showed community similarity distance decay patterns, the trend for vertebrates was the weakest. Cyanobacteria, diatom, and invertebrate community compositions were significantly correlated with several environmental factors, while the vertebrate community was only correlated with waterway width. Variation partitioning analysis indicated that varying extents of environmental conditions and spatial factors affected community organizations for different groups. Furthermore, stochastic processes contributed prominently to the microorganisms' community assembly (Sloan's neutral model R2 = 0.77 for cyanobacteria and 0.73 for diatoms) but were less important for macroorganisms (R2 = 0.21 for invertebrates and 0.15 for vertebrates). That trend was further substantiated by modified stochasticity ratio analyses. This study provides the first holistic picture of the diverse biotic communities residing in a series of hydrologically connected glacier-influenced habitats. Our results both uncovered the distinct mechanisms that underlie the metacommunity organizations of different glacial organisms and helped comprehensively predict the ecological impacts of the world's melting glaciers.
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Affiliation(s)
- Qi Lu
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Si-Yu Zhang
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jianqing Du
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Liu
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Chunxia Dong
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Chinese Academy of Sciences, Beijing, 100101, China.
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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Kulaš A, Žutinić P, Gulin Beljak V, Kepčija RM, Perić MS, Orlić S, Petrić IS, Marković T, Gligora Udovič M. Diversity of protist genera in periphyton of tufa-depositing karstic river. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-023-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Abstract
Purpose
In aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.
Methods
Protist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.
Results
The three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.
Conclusion
The combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.
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Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River. Microorganisms 2022; 10:microorganisms10122493. [PMID: 36557746 PMCID: PMC9783291 DOI: 10.3390/microorganisms10122493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.
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