1
|
Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol 2024; 26:e16619. [PMID: 38649189 DOI: 10.1111/1462-2920.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Abstract
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
Collapse
Affiliation(s)
- Megan Gross
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| |
Collapse
|
2
|
Leontidou K, Abad-Recio IL, Rubel V, Filker S, Däumer M, Thielen A, Lanzén A, Stoeck T. Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection. Environ Microbiol 2023; 25:3484-3501. [PMID: 37974518 DOI: 10.1111/1462-2920.16530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.
Collapse
Affiliation(s)
- Kleopatra Leontidou
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Ion L Abad-Recio
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
| | - Verena Rubel
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Sabine Filker
- Molecular Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Martin Däumer
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Alexander Thielen
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Anders Lanzén
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| |
Collapse
|
3
|
Leontidou K, Rubel V, Stoeck T. Comparing quantile regression spline analyses and supervised machine learning for environmental quality assessment at coastal marine aquaculture installations. PeerJ 2023; 11:e15425. [PMID: 37334127 PMCID: PMC10274583 DOI: 10.7717/peerj.15425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/25/2023] [Indexed: 06/20/2023] Open
Abstract
Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. However, this is a time-consuming and expensive method with low upscaling potential. A more rapid, inexpensive, and robust method to infer the environmental quality of marine environments is eDNA metabarcoding of bacterial communities. To infer the environmental quality of coastal habitats from metabarcoding data, two taxonomy-free approaches have been successfully applied for different geographical regions and monitoring goals, namely quantile regression splines (QRS) and supervised machine learning (SML). However, their comparative performance remains untested for monitoring the impact of organic enrichment introduced by aquaculture on marine coastal environments. We compared the performance of QRS and SML using bacterial metabarcoding data to infer the environmental quality of 230 aquaculture samples collected from seven farms in Norway and seven farms in Scotland along an organic enrichment gradient. As a measure of environmental quality, we used the Infaunal Quality Index (IQI) calculated from benthic macrofauna data (reference index). The QRS analysis plotted the abundance of amplicon sequence variants (ASVs) as a function to the IQI from which the ASVs with a defined abundance peak were assigned to eco-groups and a molecular IQI was subsequently calculated. In contrast, the SML approach built a random forest model to directly predict the macrofauna-based IQI. Our results show that both QRS and SML perform well in inferring the environmental quality with 89% and 90% accuracy, respectively. For both geographic regions, there was high correspondence between the reference IQI and both the inferred molecular IQIs (p < 0.001), with the SML model showing a higher coefficient of determination compared to QRS. Among the 20 most important ASVs identified by the SML approach, 15 were congruent with the good quality spline ASV indicators identified via QRS for both Norwegian and Scottish salmon farms. More research on the response of the ASVs to organic enrichment and the co-influence of other environmental parameters is necessary to eventually select the most powerful stressor-specific indicators. Even though both approaches are promising to infer environmental quality based on metabarcoding data, SML showed to be more powerful in handling the natural variability. For the improvement of the SML model, addition of new samples is still required, as background noise introduced by high spatio-temporal variability can be reduced. Overall, we recommend the development of a powerful SML approach that will be onwards applied for monitoring the impact of aquaculture on marine ecosystems based on eDNA metabarcoding data.
Collapse
|
4
|
Wu S, Dong Y, Stoeck T, Wang S, Fan H, Wang Y, Zhuang X. Geographic characteristics and environmental variables determine the diversities and assembly of the algal communities in interconnected river-lake system. Water Res 2023; 233:119792. [PMID: 36868116 DOI: 10.1016/j.watres.2023.119792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Algal blooms in lakes are a major hazard worldwide. Although various geographical and environmental patterns affect algal communities during river-lake transit, a thorough understanding of what patterns shape the algal communities is still rarely researched, particularly in complex interconnected river-lake systems. In this study, focusing on the most typical interconnected river-lake system in China, the Dongting Lake, we collected paired water and sediment samples in summer, when algal biomass and growth rate are at high levels. Based on 23S rRNA gene sequencing, we investigated the heterogeneity and the differences in assembly mechanisms of planktonic and benthic algae in Dongting Lake. Planktonic algae contained more Cyanobacteria and Cryptophyta, while sediment harbored higher proportions of Bacillariophyta and Chlorophyta. For planktonic algae, stochastic dispersal dominated the assembly of the communities. Upstream rivers and confluences were important sources of planktonic algae in lakes. Meanwhile, for benthic algae, deterministic environmental filtering shaped the communities, and the proportion of benthic algae exploded with increasing N:P ratio and Cu concentration until reaching thresholds of 1.5 and 0.013 g/kg respectively, and then started falling, showing non-linear responses. This study revealed the variability of different aspects of algal communities in different habitats, traced the main sources of planktonic algae, and identified the thresholds for benthic algal shifts in response to environmental filters. Hence, upstream and downstream monitoring as well as thresholds of environmental factors should be considered in further aquatic ecological monitoring or regulatory programs of harmful algal blooms in these complex systems.
Collapse
Affiliation(s)
- Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Thorsten Stoeck
- Department of Ecology, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
5
|
Wilding TA, Stoeck T, Morrissey BJ, Carvalho SF, Coulson MW. Maximising signal-to-noise ratios in environmental DNA-based monitoring. Sci Total Environ 2023; 858:159735. [PMID: 36349630 DOI: 10.1016/j.scitotenv.2022.159735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/26/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Man's impacts on global ecosystems are increasing and there is a growing demand that these activities be appropriately monitored. Monitoring requires measurement of a response metric ('signal') that changes maximally and consistently in response to the monitored activity irrespective of other factors ('noise'), thus maximising the signal-to-noise ratio. Indices derived from time-consuming morphology-based taxonomic identification of organisms are a core part of many monitoring programmes. Metabarcoding is an alternative to morphology-based identification and involves the sequencing of short fragments of DNA ('markers') from multiple taxa simultaneously. DNA suitable for metabarcoding includes that extracted from environmental samples (eDNA). Metabarcoding outputs DNA sequences that can be identified (annotated) by matching them against archived annotated sequences. However, sequences from most organisms are not archived - preventing annotation and potentially limiting metabarcoding in monitoring applications. Consequently, there is growing interest in using unannotated sequences as response metrics in monitoring programmes. We compared the sequences from three commonly used markers (16S (V3/V4 regions), 18S (V1/V2 regions) and COI) and, sampling along steep impact gradients, showed that the 16S and COI sequences were associated with the largest and smallest signal-to-noise ratio respectively. We trialled four separate, intuitive, noise-reduction approaches and demonstrated that removing less frequent sequences improved the signal-to-noise ratio, partitioning an additional 25 % from noise to explanatory factors in non-parametric ANOVA (NPA) and reducing dispersion in the data. For the 16S marker, retaining only the most frequently observed sequence, per sample, resulting in nine sequences across 150 samples, generated a near-maximal signal-to-noise ratio (95 % of the variance explained in NPA). We recommend that NPA, combined with rigorous elimination of less frequent sequences, be used to pre-filter sequences/taxa being used in monitoring applications. Our approach will simplify downstream analysis, for example the identification of key taxa and functional associations.
Collapse
Affiliation(s)
- Thomas A Wilding
- Scottish Association for Marine Science, Dunbeg, OBAN, PA34 1QA, UK.
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Dept. of Ecology, D-67663 Kaiserslautern, Germany
| | - Barbara J Morrissey
- Institute for Biodiversity and Freshwater Conservation, UHI Inverness, Inverness IV2 5NA, UK
| | | | - Mark W Coulson
- Institute for Biodiversity and Freshwater Conservation, UHI Inverness, Inverness IV2 5NA, UK
| |
Collapse
|
6
|
Oladi M, Leontidou K, Stoeck T, Shokri MR. Environmental DNA-based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf. Mar Pollut Bull 2022; 184:114143. [PMID: 36182786 DOI: 10.1016/j.marpolbul.2022.114143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.
Collapse
Affiliation(s)
- Mahshid Oladi
- Technische Universität Kaiserslautern, Ecology Group, Kaiserslautern, Germany; Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Kleopatra Leontidou
- Technische Universität Kaiserslautern, Ecology Group, Kaiserslautern, Germany
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology Group, Kaiserslautern, Germany
| | - Mohammad Reza Shokri
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C., Evin, Tehran, Iran.
| |
Collapse
|
7
|
Dong J, Liu Y, Ma J, Ma H, Stoeck T, Fan X. Ultrastructure of Diophrys appendiculata and new systematic consideration of the euplotid family Uronychiidae (Protista, Ciliophora). Mar Life Sci Technol 2022; 4:551-568. [PMID: 37078077 PMCID: PMC10077282 DOI: 10.1007/s42995-022-00153-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/13/2022] [Indexed: 05/03/2023]
Abstract
The ultrastructure of ciliates carries important cytological, taxonomical, and evolutionary signals for these single-celled eukaryotic organisms. However, little ultrastructural data have been accumulated for most ciliate groups with systematic problems. In the present work, a well-known marine uronychiid, Diophrys appendiculata, was investigated using electron microscopy and a comparison with, and a discussion considering, phylogenetic analyses were made. The new findings primarily show that: (i) this species lacks the typical alveolar plate, bears cortical ampule-like extrusomes, and has microtubular triads in the dorsal pellicle, and thus exhibits some ultrastructural features in common with most of its previously studied congeners; (ii) each adoral membranelle before the level of frontal cirrus II/2 contains three rows of kinetosomes and each membranelle after the level of frontal cirrus II/2 contains four rows, which might be related with morphogenesis and could be considered as a distinctive character of Diophrys; (iii) some structural details of the buccal field, such as the extra-pellicular fibrils, pellicle, pharyngeal disks and microtubular sheet, were documented. In addition, based on the ultrastructural comparison of representatives, we discuss the differentiation between the subfamilies Diophryinae and Uronychiinae. A hypothetical systematic relationship of members in the order Euplotida based on a wide range of data is also provided.
Collapse
Affiliation(s)
- Jingyi Dong
- School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
| | - Yujie Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Jiyang Ma
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Thorsten Stoeck
- Ecology Group, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, 200241 China
| |
Collapse
|
8
|
Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Sci Total Environ 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
Collapse
Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
| |
Collapse
|
9
|
Chen L, Ren Y, Han K, Stoeck T, Jiang J, Pan H. Re-description and molecular phylogeny of the free-swimming peritrichs Hastatella radians and H. aesculacantha (Ciliophora, Peritrichia) from china. Eur J Protistol 2022; 84:125891. [DOI: 10.1016/j.ejop.2022.125891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/03/2022]
|
10
|
Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2022; 24:983. [PMID: 35212451 DOI: 10.1111/1462-2920.15954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Frantal D, Agatha S, Beisser D, Boenigk J, Darienko T, Dirren-Pitsch G, Filker S, Gruber M, Kammerlander B, Nachbaur L, Scheffel U, Stoeck T, Qian K, Weißenbacher B, Pröschold T, Sonntag B. Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution. Front Microbiol 2022; 12:787290. [PMID: 35185817 PMCID: PMC8854374 DOI: 10.3389/fmicb.2021.787290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.
Collapse
Affiliation(s)
- Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Tatyana Darienko
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Experimental Phycology and Culture Collection of Algae, University of Göttingen, Göttingen, Germany
| | - Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Sabine Filker
- Molecular Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | | | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Federal Agency for Water Management, Institute for Aquatic Ecology and Fisheries Management, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Ulrike Scheffel
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Kuimei Qian
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- College of Environmental Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Birgit Weißenbacher
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- *Correspondence: Bettina Sonntag,
| |
Collapse
|
12
|
Lian C, Wang Y, Jiang J, Yuan Q, Al-Farraj SA, El-Serehy HA, Song W, Stoeck T, Shao C. Euplotes huizhouensis nom. nov. (Ciliophora, Euplotida), a replacement name for the junior primary homonym Euplotes tuffraui. Eur J Protistol 2022; 83:125867. [DOI: 10.1016/j.ejop.2022.125867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 11/24/2022]
|
13
|
Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I, Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. Mar Pollut Bull 2021; 173:113129. [PMID: 34784523 DOI: 10.1016/j.marpolbul.2021.113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures serving as bioindicators has gone untested. We compared eDNA metabarcoding results of marine bacterial communities from sample aliquots that were treated with a nucleic acid preservation solution (treated samples) and aliquots that were frozen without further treatment (non-treated samples). Sediment samples were obtained from coastal locations subjected to different stressors (aquaculture, urbanization, industry). DNA extraction efficiency, bacterial community profiles, and measures of alpha- and beta-diversity were highly congruent between treated and non-treated samples. As both preservation methods provide the same relevant information to environmental managers and regulators, we recommend the inclusion of both methods into SOPs for biomonitoring in marine coastal environments.
Collapse
Affiliation(s)
- Verena Dully
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Giulia Rech
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, United Kingdom
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Iain Berrill
- Scottish Salmon Producers Organization, Edinburgh, Scotland, United Kingdom
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany.
| |
Collapse
|
14
|
Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2021; 23:4778-4796. [PMID: 34258839 DOI: 10.1111/1462-2920.15668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/12/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.
Collapse
Affiliation(s)
- Changyu Zhu
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.,Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weiwei Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, and Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Yusen Xu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Oceanography, College of Science, Port Said University, Port Said, 42511, Egypt
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhenzhen Yi
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| |
Collapse
|
15
|
Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Collapse
Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
| |
Collapse
|
16
|
Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
Collapse
Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
17
|
Dully V, Wilding TA, Mühlhaus T, Stoeck T. Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning. Comput Struct Biotechnol J 2021; 19:2256-2268. [PMID: 33995917 PMCID: PMC8093828 DOI: 10.1016/j.csbj.2021.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental DNA metabarcoding is a powerful approach for use in biomonitoring and impact assessments. Amplicon-based eDNA sequence data are characteristically highly divergent in sequencing depth (total reads per sample) as influenced inter alia by the number of samples simultaneously analyzed per sequencing run. The random forest (RF) machine learning algorithm has been successfully employed to accurately classify unknown samples into monitoring categories. To employ RF to eDNA data, and avoid sequencing-depth artifacts, sequence data across samples are normalized using rarefaction, a process that inherently loses information. The aim of this study was to inform future sampling designs in terms of the relationship between sampling depth and RF accuracy. We analyzed three published and one new bacterial amplicon datasets, using a RF, based initially on the maximal rarefied data available (minimum mean of > 30,000 reads across all datasets) to give our baseline performance. We then evaluated the RF classification success based on increasingly rarefied datasets. We found that extreme to moderate rarefaction (50-5000 sequences per sample) was sufficient to achieve prediction performance commensurate to the full data, depending on the classification task. We did not find that the number of classification classes, data balance across classes, or the total number of sequences or samples, were associated with predictive accuracy. We identified the ability of the training data to adequately characterize the classes being mapped as the most important criterion and discuss how this finding can inform future sampling design for eDNA based biomonitoring to reduce costs and computation time.
Collapse
Key Words
- 16S rRNA
- AMBI, AZTI's marine biotic index
- ASV, Amplicon Sequence Variants
- AZE, allowable zone of effect, intermediate impact zone
- BI, biotic index
- BallWa, ballast water dataset
- BasCo, Basque coast dataset
- Biomonitoring
- CE, cage edge
- CV, Coefficient of Variance
- DADA2, Divisive Amplicon Denoising Algorithm
- EQ, environmental quality
- Environmental DNA
- FM, full model
- MDS, multidimensional scaling
- Machine learning
- Marine
- NEB, New England Biolabs
- NW, north west
- NorSa, Norway salmon dataset
- OOB-error, out-of-bag error estimate
- PCR, polymerase chain reaction
- REF, reference site
- RF, random forest algorithm
- SML, supervised machine learning
- ScoSa, Scottish salmon farm dataset
- V3-V4, hypervariable gene regions of the 16s rRNA
- bp, base pairs
- eDNA, environmental deoxyribonucleic acid
- microgAMBI, AZTI's marine biotic index based on microbial genes
- mtry, numbers of variables tried at each split
- n, number
- rRNA, small subunit prokaryotic ribosomal ribonucleic acid
Collapse
Affiliation(s)
- Verena Dully
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Thomas A. Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, United Kingdom
| | - Timo Mühlhaus
- Technische Universität Kaiserslautern, Computational Systems Biology, D-67663 Kaiserslautern, Germany
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
- Corresponding author.
| |
Collapse
|
18
|
Forster D, Qu Z, Pitsch G, Bruni EP, Kammerlander B, Pröschold T, Sonntag B, Posch T, Stoeck T. Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network. Microorganisms 2021; 9:microorganisms9030549. [PMID: 33800927 PMCID: PMC8001626 DOI: 10.3390/microorganisms9030549] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 11/23/2022] Open
Abstract
Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Water temperature belonged to the strongest environmental parameters splitting the data into two distinct seasonal networks (October–April; May–September). The expected ecological niche of phytoplankton, weakened through nutrient depletion because of permanent thermal stratification and through parasitic fungi, was occupied by the cyanobacterium Planktothrix rubescens and mixotrophic nanoflagellates. Instead of phytoplankton, bacteria and nanoflagellates were the main prey organisms associated with key predators (ciliates), which contrasts traditional views of biological associations in lake plankton. In a species extinction scenario, the warm season network emerged as more vulnerable than the cold season network, indicating a time-lagged effect of warmer winter temperatures on the communities. We conclude that climate stressors compromise lake ecosystem robustness and resilience through species replacement, richness differences, and succession as indicated by key network properties.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, D-67633 Kaiserslautern, Germany; (D.F.); (Z.Q.)
| | - Zhishuai Qu
- Department of Ecology, University of Kaiserslautern, D-67633 Kaiserslautern, Germany; (D.F.); (Z.Q.)
| | - Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802 Zurich, Switzerland; (G.P.); (E.P.B.); (T.P.)
| | - Estelle P. Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802 Zurich, Switzerland; (G.P.); (E.P.B.); (T.P.)
- Laboratory of Soil Biodiversity, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Barbara Kammerlander
- Research Department for Limnology, University of Innsbruck, A-5310 Mondsee, Austria; (B.K.); (T.P.); (B.S.)
| | - Thomas Pröschold
- Research Department for Limnology, University of Innsbruck, A-5310 Mondsee, Austria; (B.K.); (T.P.); (B.S.)
| | - Bettina Sonntag
- Research Department for Limnology, University of Innsbruck, A-5310 Mondsee, Austria; (B.K.); (T.P.); (B.S.)
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802 Zurich, Switzerland; (G.P.); (E.P.B.); (T.P.)
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, D-67633 Kaiserslautern, Germany; (D.F.); (Z.Q.)
- Correspondence: ; Tel.: +49-631-205-2502; Fax: +49-631-2051-32496
| |
Collapse
|
19
|
Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Res 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
Collapse
Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| |
Collapse
|
20
|
Lian C, Wang Y, Jiang J, Yuan Q, Al-Farraj SA, El-Serehy HA, Song W, Stoeck T, Shao C. Systematic positions and taxonomy of two new ciliates found in China: Euplotes tuffraui sp. nov. and E. shii sp. nov. (Alveolata, Ciliophora, Euplotida). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2020.1865472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Chunyu Lian
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119, China
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China
| | - Qingxiang Yuan
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Saleh A. Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Hamed A. El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119, China
| |
Collapse
|
21
|
Qu Z, Forster D, Bruni EP, Frantal D, Kammerlander B, Nachbaur L, Pitsch G, Posch T, Pröschold T, Teubner K, Sonntag B, Stoeck T. Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility. Mol Ecol 2020; 30:1053-1071. [PMID: 33306859 DOI: 10.1111/mec.15776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022]
Abstract
Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co-occurrence networks constructed from time-series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate-specific subnetworks resembled autecological species-specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co-occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate-stressed ecosystems.
Collapse
Affiliation(s)
- Zhishuai Qu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Estelle P Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Katrin Teubner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
22
|
Qu Z, Weinisch L, Fan X, Katzenmeier S, Stoeck T, Filker S. Morphological, Phylogenetic and Ecophysiological Characterization of a New Ciliate, Platynematum rossellomorai n. sp. (Oligohymenophorea, Scuticociliatia), Detected in a Hypersaline Pond on Mallorca, Spain. Protist 2020; 171:125751. [PMID: 32890795 DOI: 10.1016/j.protis.2020.125751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/29/2022]
Abstract
With highly specialized morphology and unexplored functional capacities, ciliates from extreme habitats are drawing increasing attention. During a microbial investigation of a solar saltern pond (salinity 240‰) on Mallorca, Spain, a previously unknown scuticociliate, Platynematum rossellomorai n. sp. was isolated, cultured and studied using a tripartite approach consisting of a morphological description, a molecular analysis and an ecophysiological characterization. The ciliate has distinct morphological characteristics and its main diagnostic features include a large anteriorly positioned oral area (occupying almost half of the body length), two caudal cilia and a small number of somatic kineties. However, due to the most important generic feature of Cinetochilidae, the consistency of the arrangement of the adoral membranes, the ciliate is classified as a new member of the genus Platynematum. Its 18S rRNA gene sequence shows a sequence similarity of 91.0% to the closest deposited relative, Platynematum salinarum, and a phylogenetic analysis reveals a close relationship to other members of the family Cinetochilidae Perty, 1852. Growth experiments identify the ciliate as a borderline halophile, with a tolerance range between 180 and 280‰ salinity. The ciliate apparently accumulates the compatible solutes glycine betaine and ectoine to counterbalance osmotic stress, however, other osmoregulatory mechanisms are not excluded.
Collapse
Affiliation(s)
- Zhishuai Qu
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Lea Weinisch
- Department of Molecular Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241, PR China
| | - Sven Katzenmeier
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
| |
Collapse
|
23
|
Filker S, Stoeck T. Report of the 2020 meeting of the German Society for Protozoology. Eur J Protistol 2020; 75:125702. [PMID: 32451214 DOI: 10.1016/j.ejop.2020.125702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sabine Filker
- Department of Molecular Ecology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany.
| | - Thorsten Stoeck
- Department of Ecology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| |
Collapse
|
24
|
Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA, Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol Ecol 2020; 30:2988-3006. [PMID: 32285497 DOI: 10.1111/mec.15434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
Abstract
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
Collapse
Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics Ltd, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Thomas A Wilding
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
25
|
Forster D, Lentendu G, Filker S, Dubois E, Wilding TA, Stoeck T. Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants. Environ Microbiol 2019; 21:4109-4124. [PMID: 31361938 DOI: 10.1111/1462-2920.14764] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
Abstract
Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high-throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina-sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second-level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM-SSNs, NSC numbers decreased from 7.9-fold overestimation without abundance filter, to 4.5-fold overestimation when an abundance filter was applied. For the DADA2-SSN approach, NSC numbers decreased from 3.5-fold to 3-fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2-SSNs and SWARM-SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Elyssa Dubois
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, UK
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
26
|
Qu Z, Groben R, Marteinsson V, Agatha S, Filker S, Stoeck T. Redescription of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 (Ciliophora, Oligohymenophorea) from a Hot Spring in Iceland with Identification Key for Dexiotricha species. ACTA PROTOZOOL 2019; 57:95-106. [PMID: 31168161 DOI: 10.4467/16890027ap.18.009.8983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We isolated an encysted ciliate from a geothermal field in Iceland. The morphological features of this isolate fit the descriptions of Dexiotricha colpidiopsis Kahl, 1926) Jankowski, 1964 very well. These comprise body shape and size in vivo, the number of somatic kineties, and the positions of macronucleus and contractile vacuole. Using state-of-the-art taxonomic methods, the species is redescribed, including phylogenetic analyses of the small subunit ribosomal RNA (SSU rRNA) gene as molecular marker. In the phylogenetic analyses, D. colpidiopsis clusters with the three available SSU rRNA gene sequences of congeners, suggesting a monophyly of the genus Dexiotricha. Its closest relative in phylogenetic analyses is D. elliptica, which also shows a high morphological similarity. This is the first record of a Dexiotricha species from a hot spring, indicating a wide temperature tolerance of this species at least in the encysted state. The new findings on D. colpidiopsis are included in a briefly revision of the scuticociliate genus Dexiotricha and an identification key to the species.
Collapse
Affiliation(s)
- Zhishuai Qu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - René Groben
- Exploration & Utilization of Genetic Resources, Matis ohf., Reykjavik, Iceland
| | - Viggó Marteinsson
- Exploration & Utilization of Genetic Resources, Matis ohf., Reykjavik, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
| | - Sabine Agatha
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslauten, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
27
|
Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring. Trends Microbiol 2019; 27:387-397. [DOI: 10.1016/j.tim.2018.10.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
|
28
|
Zayed A, Kovacheva M, Muffler K, Breiner HW, Stoeck T, Ulber R. Induction and genetic identification of a callus-like growth developed in the brown alga Fucus vesiculosus. Eng Life Sci 2019; 19:363-369. [PMID: 32625015 DOI: 10.1002/elsc.201800211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/23/2019] [Accepted: 03/16/2019] [Indexed: 11/05/2022] Open
Abstract
Induction of an axenic filamentous-like callus growth from the brown algae Fucus vesiculosus is described. Different treatments were investigated in various combinations to develop axenic cultures based on identification of surface symbionts via 18S ribosomal RNA. Moreover, viability was confirmed after such processes by 2,3,5-triphenyl tetrazolium chloride assay that demonstrated an average viability of 29%, relative to nonsterilized explants. After six weeks of a phototrophic cultivation on artificial sea water-12-nitrilotriacetic acid (0.5% w/v agar), a filamentous-like callus growth was observed, which was identified genetically through its mitochondrial DNA after subculturing. Achievement of confirmed marine callus cultures might enrich old previously established blue biotechnology techniques and open new chances for cultivation of brown algae for production of good manufacturing practice-compliant bioproducts.
Collapse
Affiliation(s)
- Ahmed Zayed
- Department of Mechanical and Process Engineering Institute of Bioprocess Engineering Technical University of Kaiserslautern Kaiserslautern Germany.,Department of Pharmacognosy College of Pharmacy Tanta University Tanta Egypt
| | - Mariya Kovacheva
- Department of Mechanical and Process Engineering Institute of Bioprocess Engineering Technical University of Kaiserslautern Kaiserslautern Germany
| | - Kai Muffler
- Department of Life Sciences and Engineering University of Applied Sciences Bingen Bingen Germany
| | - Hans-Werner Breiner
- Department of Biology Institute of Ecology Technical University of Kaiserslautern Kaiserslautern Germany
| | - Thorsten Stoeck
- Department of Biology Institute of Ecology Technical University of Kaiserslautern Kaiserslautern Germany
| | - Roland Ulber
- Department of Mechanical and Process Engineering Institute of Bioprocess Engineering Technical University of Kaiserslautern Kaiserslautern Germany
| |
Collapse
|
29
|
Pitsch G, Bruni EP, Forster D, Qu Z, Sonntag B, Stoeck T, Posch T. Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts? Front Microbiol 2019; 10:248. [PMID: 30837972 PMCID: PMC6389714 DOI: 10.3389/fmicb.2019.00248] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
Ciliates represent central nodes in freshwater planktonic food webs, and many species show pronounced seasonality, with short-lived maxima of a few dominant taxa while many being rare or ephemeral. These observations are primarily based on morphospecies counting methods, which, however, have limitations concerning the amount and volume of samples that can be processed. For high sampling frequencies at large scales, high throughput sequencing (HTS) of freshwater ciliates seems to be a promising tool. However, several studies reported large discrepancy between species abundance determinations by molecular compared to morphological means. Therefore, we compared ciliate DNA metabarcodes (V9 regions of the 18S rRNA gene) with morphospecies counts for a 3-year study (Lake Zurich, Switzerland; biweekly sampling, n = 74). In addition, we isolated, cultivated and sequenced the 18S rRNA gene of twelve selected ciliate species that served as seeds for HTS analyses. This workflow allowed for a detailed comparison of V9 data with microscopic analyses by quantitative protargol staining (QPS). The dynamics of V9 read abundances over the seasonal cycle corroborated well with morphospecies population patterns. Annual successions of rare and ephemeral species were more adequately characterized by V9 reads than by QPS. However, numbers of species specific sequence reads only partly reflected rank orders seen by counts. In contrast, biomass-based assemblage compositions showed higher similarity to V9 read numbers, probably indicating a relation between cell sizes and numbers / sizes of macronuclei (or 18S rRNA operons). Full-length 18S rRNA sequences of ciliates assigned to certain morphospecies are urgently needed for barcoding approaches as planktonic taxa are still poorly represented in public databases and the interpretation of HTS data depends on profound reference sequences. Through linking operational taxonomic units (OTUs) with known morphospecies, we can use the deep knowledge about the autecology of these species.
Collapse
Affiliation(s)
- Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Estelle Patricia Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Dominik Forster
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Zhishuai Qu
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| |
Collapse
|
30
|
Li F, Qu Z, Luo D, Filker S, Hu X, Stoeck T. Morphology, Morphogenesis and Molecular Phylogeny of a New Obligate Halophile Ciliate, Schmidtiella ultrahalophila gen. nov., spec. nov. (Ciliophora, Hypotrichia) Isolated from a Volcanic Crater on Sal (Cape Verde Islands). J Eukaryot Microbiol 2019; 66:694-706. [PMID: 30657224 DOI: 10.1111/jeu.12714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 11/27/2022]
Abstract
A new hypotrichous ciliate, Schmidtiella ultrahalophila gen. nov., spec. nov., was isolated from a solar saltern on the island of Sal, Cape Verde. The possession of only one short dorsal kinety clearly distinguishes S. ultrahalophila from other known hypotrichous genera and species. Further diagnostic characters include: a flexible and slender body, an average size of 85 × 15 μm in vivo; a bipartite adoral zone with two hypertrophied frontal adoral membranelles and nine to twelve ventral adoral membranelles; three frontal, one parabuccal, two frontoventral, two or three postoral ventral, and two or three frontoterminal cirri; and marginal cirral rows variable in number, usually one on each side. Ontogenetic data indicate the following: the frontal-ventral cirri originate from six or five anlagen; the proter inherits the parental adoral zone; the frontal and ventral cirri originate from five or six anlagen; and the marginal cirral rows and the dorsal kinety tend to originate intrakinetally. Additional marginal rows are rarely derived from de novo anlagen. Based on its morphology, morphogenesis and its SSU rRNA phylogenetic placement, the new species should be assigned to the order Sporadotrichida Fauré-Fremiet, 1961. Due to low taxon sampling, however, its exact position in this order remains enigmatic.
Collapse
Affiliation(s)
- Fengchao Li
- College of Life Sciences, Hebei University, Baoding, 071002, China.,Ecology Group, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhishuai Qu
- Ecology Group, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Dan Luo
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Sabine Filker
- Molecular Ecology Group, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Xiaozhong Hu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Ecology Group, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| |
Collapse
|
31
|
Fotedar R, Stoeck T, Filker S, Fell JW, Agatha S, Al Marri M, Jiang J. Corrigendum to “Description of the HalophileEuplotes qatarensisnov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar”. J Eukaryot Microbiol 2019; 66:370-371. [DOI: 10.1111/jeu.12710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre; Ministry of Environment; 7634 Doha Qatar
| | - Thorsten Stoeck
- Department of Ecology; University of Kaiserslautern; D-67633 Kaiserslautern Germany
| | - Sabine Filker
- Department of Ecology; University of Kaiserslautern; D-67633 Kaiserslautern Germany
| | - Jack W. Fell
- Department of Marine Biology and Ecology; RSMAS/MBF, University of Miami; Miami Florida 33149
| | - Sabine Agatha
- Department of Ecology and Evolution; University of Salzburg; Hellbrunnerstrasse 34 A-5020 Salzburg Austria
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre; Ministry of Environment; 7634 Doha Qatar
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, National Demonstration Center for Experimental Fisheries Science Education; Shanghai Ocean University; Shanghai 201306 China
| |
Collapse
|
32
|
Filker S, Kühner S, Heckwolf M, Dierking J, Stoeck T. A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea. Environ Microbiol 2019; 21:603-617. [PMID: 30548156 DOI: 10.1111/1462-2920.14502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/03/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022]
Abstract
Remane's Artenminimum at the horohalinicum is a fundamental concept in ecology to describe and explain the distribution of organisms along salinity gradients. However, a recent metadata analysis challenged this concept for protists, proposing a species maximum in brackish waters. Due to data bias, this literature-based investigation was highly discussed. Reliable data verifying or rejecting the species minimum for protists in brackish waters were critically lacking. Here, we sampled a pronounced salinity gradient along a west-east transect in the Baltic Sea and analysed protistan plankton communities using high-throughput eDNA metabarcoding. A strong salinity barrier at the upper limit of the horohalinicum and 10 psu appeared to select for significant shifts in protistan community structures, with dinoflagellates being dominant at lower salinities, and dictyochophytes and diatoms being keyplayers at higher salinities. Also in vertical water column gradients in deeper basins (Kiel Bight, Arkona and Bornholm Basin) appeared salinity as significant environmental determinant influencing alpha- and beta-diversity patterns. Importantly, alpha-diversity indices revealed species maxima in brackish waters, that is, indeed contrasting Remane's Artenminimum concept. Statistical analyses confirmed salinity as the major driving force for protistan community structuring with high significance. This suggests that macrobiota and microbial eukaryotes follow fundamentally different rules regarding diversity patterns in the transition zone from freshwater to marine waters.
Collapse
Affiliation(s)
- Sabine Filker
- Molecular Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Steffen Kühner
- Molecular Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Melanie Heckwolf
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Jan Dierking
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Thorsten Stoeck
- Ecology Group, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| |
Collapse
|
33
|
Stoeck T, Pan H, Dully V, Forster D, Jung T. Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants. Water Res 2018; 144:322-331. [PMID: 30053623 DOI: 10.1016/j.watres.2018.07.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Knowledge-driven management for wastewater treatment plant (WWTP) performance becomes increasingly important considering the globally growing production of wastewater and the rising demand of clean water supply. Even though the potential of microbial organisms (bacteria and protists) as bioindicators for WWTP performance is well known, it is far from being fully exploited for routine monitoring programs. Therefore, we here used massive sequencing of environmental (e)DNA metabarcodes from bacterial (V3-V4 region of the SSU rRNA gene) and eukaryote (V9 region of the SSU rRNA gene) communities in 21 activated sludge samples obtained from full-scale municipal WWTPs in Germany. Microbial community patterns were compared to standard WWTP operating parameters and two traditionally used WWTP performance indicators (Sludge Biotic Index and Sludge Index). Both indices showed low concordance and hardly correlated with chemical WWTP performance parameters nor did they correlate with microbial community structures. In contrast, microbial community profiles significantly correlated with WWTP performance parameters and operating conditions of the plants under study. Therefore, eDNA metabarcode profiles of whole microbial communities indicate the performance of WWTP and can provide useful information for management strategies. We here suggest a strategy for the development of an eDNA metabarcode based bioindicator system, which can be implemented in future standard monitoring programs for WWTP performance and effluent quality.
Collapse
Affiliation(s)
- Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany.
| | - Hongbo Pan
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Verena Dully
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, D-67663, Kaiserslautern, Germany
| | - Thorsten Jung
- Stadtentwässerung Kaiserslautern, D-67659, Kaiserslautern, Germany
| |
Collapse
|
34
|
Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T. A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture. J Eukaryot Microbiol 2018; 66:294-308. [DOI: 10.1111/jeu.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dominik Forster
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Sabine Filker
- Molecular Ecology; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Rebecca Kochems
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Hans-Werner Breiner
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
- ID-Gene ecodiagnostics Ltd.; Campus Biotech Innovation Park 1202 Geneva Switzerland
| | - Thorsten Stoeck
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| |
Collapse
|
35
|
Cordier T, Forster D, Dufresne Y, Martins CIM, Stoeck T, Pawlowski J. Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring. Mol Ecol Resour 2018; 18:1381-1391. [DOI: 10.1111/1755-0998.12926] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
| | - Dominik Forster
- Ecology Group; University of Kaiserslautern; Kaiserslautern Germany
| | - Yoann Dufresne
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
- Institut Pasteur - Hub of Bioinformatics and Biostatistics - C3BI; USR 3756 IP CNRS; Paris France
| | | | - Thorsten Stoeck
- Ecology Group; University of Kaiserslautern; Kaiserslautern Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
- ID-Gene ecodiagnostics, Ltd; Plan-les-Ouates Switzerland
| |
Collapse
|
36
|
Vďačný P, Rajter Ľ, Stoeck T, Foissner W. A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids. J Eukaryot Microbiol 2018; 66:167-181. [PMID: 29873141 DOI: 10.1111/jeu.12641] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 11/30/2022]
Abstract
Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology-based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free-living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction.
Collapse
Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ľubomír Rajter
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Wilhelm Foissner
- FB Ecology and Evolution, University of Salzburg, Salzburg, Austria
| |
Collapse
|
37
|
Lentendu G, Mahé F, Bass D, Rueckert S, Stoeck T, Dunthorn M. Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Mol Ecol 2018; 27:2846-2857. [PMID: 29851187 DOI: 10.1111/mec.14731] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/27/2018] [Accepted: 05/18/2018] [Indexed: 01/11/2023]
Abstract
Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests.
Collapse
Affiliation(s)
- Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany.,CIRAD, UMR LSTM, Montpellier, France
| | - David Bass
- Department of Life Sciences, The Natural History Museum London, London, UK.,Centre for Environment, Fisheries & Aquaculture Science (Cefas), Weymouth, Dorset, UK
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
38
|
Xu Y, Stoeck T, Forster D, Ma Z, Zhang L, Fan X. Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities. Mar Pollut Bull 2018; 131:646-654. [PMID: 29886992 DOI: 10.1016/j.marpolbul.2018.04.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
In this study, we tested the hypothesis that the functional diversity of benthic ciliates has high potential to monitor marine ecological status. Therefore, we investigated the spatial and temporal variation of functional diversity of benthic ciliates in the Yangtze Estuary during one year using biological traits analyses and functional diversity indices. Traits and community compositions showed clear spatial and temporal variations. Among a variety of biological traits, feeding type and body size emerged as strongest predictable variables. Functional divergence (FDiv) had an advantage over two other functional diversity indices, as well as over classical diversity measures (i.e. richness, evenness, Shannon-Wiener) to infer environmental status. Significant correlations between biological traits, FDiv and environmental variables (i.e. nutrients, temperature, salinity) suggested that functional diversity of benthic ciliates might be used as a bio-indicator in environmental status assessments. Further mandatory researches need to implement functional diversity of ciliates in routine monitoring programs were discussed.
Collapse
Affiliation(s)
- Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, Erwin Schroedinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, Erwin Schroedinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Zuhang Ma
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Liquan Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241, China.
| |
Collapse
|
39
|
Qu Z, Li L, Lin X, Stoeck T, Pan H, Al-Rasheid KAS, Song W. Diversity of the cyrtophorid genus Chlamydodon (Protista, Ciliophora): its systematics and geographic distribution, with taxonomic descriptions of three species. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1456493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zhishuai Qu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai 201306, China
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Department of Ecology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Lifang Li
- Marine College, Shandong University, Weihai 264209, China
| | - Xiaofeng Lin
- Laboratory of Protozoology, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Hongbo Pan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai 201306, China
| | - Khaled A. S. Al-Rasheid
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
40
|
Heber D, Stoeck T, Foissner W. Corrigendum: "Morphology and Ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and Molecular Phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia)" by Heber et al. 2014. J Eukaryot Microbiol 2018; 65:291-292. [PMID: 29504196 PMCID: PMC6886046 DOI: 10.1111/jeu.12487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Domingo Heber
- Department of Organismic BiologyUniversity of SalzburgHellbrunner Strasse 34Salzburg5020Austria
| | - Thorsten Stoeck
- Department of EcologyUniversity of KaiserslauternErwin‐Schrödinger Strasse 14Kaiserslautern67663Germany
| | - Wilhelm Foissner
- Department of Organismic BiologyUniversity of SalzburgHellbrunner Strasse 34Salzburg5020Austria
| |
Collapse
|
41
|
Stoeck T, Frühe L, Forster D, Cordier T, Martins CIM, Pawlowski J. Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture. Mar Pollut Bull 2018; 127:139-149. [PMID: 29475645 DOI: 10.1016/j.marpolbul.2017.11.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n=72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference data from standard macrofauna biomonitoring surveys of the same samples. Deltaproteobacteria were predominant in immediate vicinity of the salmon cages. Along the transect, significant shifts in bacterial community structures were observed with Gammaproteobacteria dominating the less-impacted sites. Alpha- and beta-diversity measures of bacterial communities correlated significantly with macrofauna diversity metrics and with five ecological status indices. Benthic bacterial communities mirror the reaction of macrofauna bioindicators to environmental disturbances caused by salmon farming. The implementation of bacterial eDNA metabarcoding in future Strategic Framework Directives is an alternative cost-effective high-throughput biomonitoring solution, providing a basis for management strategies in a matter of days rather than months.
Collapse
Affiliation(s)
- Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany.
| | - Larissa Frühe
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - Tristan Cordier
- University of Geneva, Department of Genetics and Evolution, 1211 Geneva, Switzerland
| | | | - Jan Pawlowski
- University of Geneva, Department of Genetics and Evolution, 1211 Geneva, Switzerland; ID-Gene ecodiagnostics Ltd. 1228 Plan-les-Ouates, Switzerland
| |
Collapse
|
42
|
Pan H, Stoeck T. Redescription of the halophile ciliate, Blepharisma halophilum Ruinen, 1938 (Ciliophora, Heterotrichea, Heterotrichida) shows that the genus Blepharisma is non-monophyletic. Eur J Protistol 2017; 61:20-28. [DOI: 10.1016/j.ejop.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
|
43
|
Zhao F, Filker S, Stoeck T, Xu K. Ciliate diversity and distribution patterns in the sediments of a seamount and adjacent abyssal plains in the tropical Western Pacific Ocean. BMC Microbiol 2017; 17:192. [PMID: 28899339 PMCID: PMC5596958 DOI: 10.1186/s12866-017-1103-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/05/2017] [Indexed: 01/08/2023] Open
Abstract
Background Benthic ciliates and the environmental factors shaping their distribution are far from being completely understood. Likewise, deep-sea systems are amongst the least understood ecosystems on Earth. In this study, using high-throughput DNA sequencing, we investigated the diversity and community composition of benthic ciliates in different sediment layers of a seamount and an adjacent abyssal plain in the tropical Western Pacific Ocean with water depths ranging between 813 m and 4566 m. Statistical analyses were used to assess shifts in ciliate communities across vertical sediment gradients and water depth. Results Nine out of 12 ciliate classes were detected in the different sediment samples, with Litostomatea accounting for the most diverse group, followed by Plagiopylea and Oligohymenophorea. The novelty of ciliate genetic diversity was extremely high, with a mean similarity of 93.25% to previously described sequences. On a sediment depth gradient, ciliate community structure was more similar within the upper sediment layers (0-1 and 9-10 cm) compared to the lower sediment layers (19-20 and 29-30 cm) at each site. Some unknown ciliate taxa which were absent from the surface sediments were found in deeper sediments layers. On a water depth gradient, the proportion of unique OTUs was between 42.2% and 54.3%, and that of OTUs shared by all sites around 14%. However, alpha diversity of the different ciliate communities was relatively stable in the surface layers along the water depth gradient, and about 78% of the ciliate OTUs retrieved from the surface layer of the shallowest site were shared with the surface layers of sites deeper than 3800 m. Correlation analyses did not reveal any significant effects of measured environmental factors on ciliate community composition and structure. Conclusions We revealed an obvious variation in ciliate community along a sediment depth gradient in the seamount and the adjacent abyssal plain and showed that water depth is a less important factor shaping ciliate distribution in deep-sea sediments unlike observed for benthic ciliates in shallow seafloors. Additionally, an extremely high genetic novelty of ciliate diversity was found in these habitats, which points to a hot spot for the discovery of new ciliate species. Electronic supplementary material The online version of this article (10.1186/s12866-017-1103-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Feng Zhao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China.,Department of Molecular Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Kuidong Xu
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
44
|
Qu Z, Pan H, Lin X, Li L, Aleidan AMA, Al-Farraj SA, Stoeck T, Hu X. A Contribution to the Morphology and Phylogeny of Chlamydodon, with Three New Species from China (Ciliophora, Cyrtophoria). J Eukaryot Microbiol 2017; 65:236-249. [PMID: 28888076 DOI: 10.1111/jeu.12472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/15/2017] [Accepted: 09/01/2017] [Indexed: 11/27/2022]
Abstract
Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne-like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer somatic kineties, and/or an elongated body shape. Chlamydodon crassidens sp. n. is characterized mainly by an inverted triangular body shape, a posteriorly interrupted cross-striated band (5-6 μm wide), and a large cytostome. Moreover, we provided small-subunit (SSU) rDNA sequences of C. similis sp. n. and C. oligochaetus sp. n. Maximum likelihood (ML) and Bayesian inference (BI) consistently placed C. similis sp. n. as a sister to C. paramnemosyne, but showed different branching position of C. oligochaetus sp. n., which may be due to a low taxon sampling in the Chlamydodontidae and/or an insufficient resolution of the marker gene at species level.
Collapse
Affiliation(s)
- Zhishuai Qu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Hongbo Pan
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaofeng Lin
- College of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Lifang Li
- Marine College, Shandong University, Weihai, 264209, China
| | | | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Xiaozhong Hu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| |
Collapse
|
45
|
Filker S, Forster D, Weinisch L, Mora-Ruiz M, González B, Farías ME, Rosselló-Móra R, Stoeck T. Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions. Environ Microbiol 2017; 19:3186-3200. [PMID: 28574222 DOI: 10.1111/1462-2920.13805] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/26/2017] [Indexed: 11/28/2022]
Abstract
The identification of environmental barriers which govern species distribution is a fundamental concern in ecology. Even though salt was previously identified as a major transition boundary for micro- and macroorganisms alike, the salinities causing species turnover in protistan communities are unknown. We investigated 4.5 million high-quality protistan metabarcodes (V4 region of the SSU rDNA) obtained from 24 shallow salt ponds (salinities 4%-44%) from South America and Europe. Statistical analyses of protistan community profiles identified four salinity classes, which strongly selected for different protistan communities: 4-9%, 14-24%, 27-36% and 38-44%. The proportion of organisms unknown to science is highest in the 14-24% salinity class, showing that environments within this salinity range are an unappreciated reservoir of as yet undiscovered organisms. Distinct higher-rank taxon groups dominated in the four salinity classes in terms of diversity. As increasing salinities require different cellular responses to cope with salt, our results suggest that different evolutionary lineages of protists have evolved distinct haloadaptation strategies. Salinity appears to be a stronger selection factor for the structuring of protistan communities than geography. Yet, we find a higher degree of endemism in shallow salt ponds compared with less isolated ecosystems such as the open ocean. Thus, rules for biogeographic structuring of protistan communities are not universal, but depend on the ecosystem under consideration.
Collapse
Affiliation(s)
- Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Lea Weinisch
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Merit Mora-Ruiz
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain
| | - Bernardo González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez - Center of Applied Ecology and Sustainability, Santiago de Chile, Chile
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| |
Collapse
|
46
|
Warren A, Patterson DJ, Dunthorn M, Clamp JC, Achilles‐Day UE, Aescht E, Al‐Farraj SA, Al‐Quraishy S, Al‐Rasheid K, Carr M, Day JG, Dellinger M, El‐Serehy HA, Fan Y, Gao F, Gao S, Gong J, Gupta R, Hu X, Kamra K, Langlois G, Lin X, Lipscomb D, Lobban CS, Luporini P, Lynn DH, Ma H, Macek M, Mackenzie‐Dodds J, Makhija S, Mansergh RI, Martín‐Cereceda M, McMiller N, Montagnes DJ, Nikolaeva S, Ong'ondo GO, Pérez‐Uz B, Purushothaman J, Quintela‐Alonso P, Rotterová J, Santoferrara L, Shao C, Shen Z, Shi X, Song W, Stoeck T, La Terza A, Vallesi A, Wang M, Weisse T, Wiackowski K, Wu L, Xu K, Yi Z, Zufall R, Agatha S. Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). J Eukaryot Microbiol 2017; 64:539-554. [PMID: 28061024 PMCID: PMC5697677 DOI: 10.1111/jeu.12391] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/27/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.
Collapse
Affiliation(s)
- Alan Warren
- Department of Life SciencesNatural History MuseumLondonSW7 5BDUnited Kingdom
| | | | - Micah Dunthorn
- Department of EcologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - John C. Clamp
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth Carolina27707USA
| | - Undine E.M. Achilles‐Day
- Department of Life and Environmental SciencesBournemouth UniversityBournemouthBH12 5BBUnited Kingdom
| | - Erna Aescht
- Biology Center of the Upper Austrian MuseumLinzA‐4040Austria
| | | | | | | | - Martin Carr
- Department of Biological SciencesUniversity of HuddersfieldHuddersfieldHD1 3DHUnited Kingdom
| | - John G. Day
- Scottish Association for Marine ScienceObanPA37 1QAUnited Kingdom
| | | | | | - Yangbo Fan
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Feng Gao
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Shan Gao
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Jun Gong
- Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai264003China
| | - Renu Gupta
- Maitreyi CollegeUniversity of DelhiNew Delhi110021India
| | - Xiaozhong Hu
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Komal Kamra
- SGTB Khalsa CollegeUniversity of DelhiDelhi110007India
| | - Gaytha Langlois
- Department of Science & TechnologyBryant UniversitySmithfieldRhode Island02917USA
| | - Xiaofeng Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Diana Lipscomb
- Department of Biological SciencesGeorge Washington UniversityWashingtonDistrict of Columbia20052USA
| | | | - Pierangelo Luporini
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Denis H. Lynn
- Department of Integrative BiologyUniversity of GuelphGuelphONN1G 2W1Canada
| | - Honggang Ma
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Miroslav Macek
- Tropical Limnology Research Project, FES IztacalaUniversidad National Autonoma de MéxicoEdo. México 540 90Mexico
| | | | - Seema Makhija
- Acharya Narendra Dev CollegeUniversity of DelhiNew Delhi110019India
| | - Robert I. Mansergh
- Institute of Marine SciencesUniversity of PortsmouthPortsmouthPO4 9LYUnited Kingdom
| | - Mercedes Martín‐Cereceda
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | - Nettie McMiller
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth Carolina27707USA
| | - David J.S. Montagnes
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Svetlana Nikolaeva
- Department of Earth SciencesNatural History MuseumLondonSW7 5BDUnited Kingdom
- Kazan Federal University, Kremlyovskaya ul. 18Kazan 420000Russia
| | | | - Blanca Pérez‐Uz
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | | | - Pablo Quintela‐Alonso
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | - Johana Rotterová
- Department of ZoologyCharles University in PraguePrague12744Czech Republic
| | | | - Chen Shao
- Key Laboratory of Biomedical Information EngineeringXi'an Jiaotong UniversityXi'an710049China
| | - Zhuo Shen
- Research Center of Hydrobiology, College of Life Science and TechnologyJinan UniversityGuangzhou510632China
| | - Xinlu Shi
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Thorsten Stoeck
- Department of EcologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Antonietta La Terza
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Mei Wang
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Thomas Weisse
- Research Institute for LimnologyUniversity of InnsbruckMondsee5310Austria
| | | | - Lei Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Kuidong Xu
- Institute of OceanologyChinese Academy of SciencesQingdao266071China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Rebecca Zufall
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexas77006‐5001USA
| | - Sabine Agatha
- Department of Ecology and EvolutionUniversity of SalzburgSalzburgA‐5020Austria
| |
Collapse
|
47
|
Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WHCF, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T. Benthic protists: the under-charted majority. FEMS Microbiol Ecol 2016; 92:fiw120. [PMID: 27267932 DOI: 10.1093/femsec/fiw120] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Fréderic Mahé
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - John R Dolan
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - David Bass
- Department of Life Sciences, the Natural History Museum London, Cromwell Road, London SW7 5BD, UK Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, the Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Lucie Bittner
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France Sorbonne Universités, UPMC, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005 Paris, France
| | - Christophe Boutte
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Richard Christen
- CNRS, UMR 7138 & Université de Nice-Sophia Antipolis, F-06103 Nice cedex 2, France Université de Nice-Sophia Antipolis & CNRS, UMR 7138 F-06103 Nice cedex 2, France
| | | | - Johan Decelle
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Bente Edvardsen
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Elianne Egge
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Wenche Eikrem
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France CNRS, UMR 8227 & UPMC Université Paris 06, Station Biologique de Roscoff, F-29682 Roscoff, France
| | | | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Fabrice Not
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, 4, Boulevard d'Yvoy, CH-1211 Geneva, Switzerland
| | - Massimo C Pernice
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Sarah Romac
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Sébastien Santini
- CNRS, Aix-Marseille Université, IGS UMR7256, F-13288 Marseille, France
| | - Diana Sarno
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Raffaele Siano
- Ifremer, Centre de Brest DYNECO/Pelagos Technopôle Brest Iroise, BP 7029280 Plouzané, France
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| |
Collapse
|
48
|
Filker S, Sommaruga R, Vila I, Stoeck T. Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns. Mol Ecol 2016; 25:2286-301. [PMID: 27029537 DOI: 10.1111/mec.13633] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/11/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022]
Abstract
Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.
Collapse
Affiliation(s)
- Sabine Filker
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Ruben Sommaruga
- Institute of Ecology, Lake and Glacier Research Group, University of Innsbruck, Innsbruck, 6020, Austria
| | - Irma Vila
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| |
Collapse
|
49
|
Abstract
Many large network data sets are noisy and contain links representing low-intensity relationships that are difficult to differentiate from random interactions. This is especially relevant for high-throughput data from systems biology, large-scale ecological data, but also for Web 2.0 data on human interactions. In these networks with missing and spurious links, it is possible to refine the data based on the principle of structural similarity, which assesses the shared neighborhood of two nodes. By using similarity measures to globally rank all possible links and choosing the top-ranked pairs, true links can be validated, missing links inferred, and spurious observations removed. While many similarity measures have been proposed to this end, there is no general consensus on which one to use. In this article, we first contribute a set of benchmarks for complex networks from three different settings (e-commerce, systems biology, and social networks) and thus enable a quantitative performance analysis of classic node similarity measures. Based on this, we then propose a new methodology for link assessment called z* that assesses the statistical significance of the number of their common neighbors by comparison with the expected value in a suitably chosen random graph model and which is a consistently top-performing algorithm for all benchmarks. In addition to a global ranking of links, we also use this method to identify the most similar neighbors of each single node in a local ranking, thereby showing the versatility of the method in two distinct scenarios and augmenting its applicability. Finally, we perform an exploratory analysis on an oceanographic plankton data set and find that the distribution of microbes follows similar biogeographic rules as those of macroorganisms, a result that rejects the global dispersal hypothesis for microbes.
Collapse
Affiliation(s)
- Andreas Spitz
- Institute of Computer Science, Heidelberg University, Heidelberg, BW, Germany
| | - Anna Gimmler
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, RP, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, RP, Germany
| | - Katharina Anna Zweig
- Department of Computer Science, University of Kaiserslautern, Kaiserslautern, RP, Germany
- * E-mail:
| | - Emőke-Ágnes Horvát
- Northwestern Institute on Complex Systems (NICO), Northwestern University, Evanston, IL, United States of America
| |
Collapse
|
50
|
Fotedar R, Stoeck T, Filker S, Fell JW, Agatha S, Al Marri M, Jiang J. Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar. J Eukaryot Microbiol 2016; 63:578-90. [PMID: 26864150 DOI: 10.1111/jeu.12305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 11/30/2022]
Abstract
The morphology, ontogenesis, and phylogenetic relationships of a halophile euplotid ciliates, Euplotes qatarensis nov. spec., isolated from the Khor Al-Adaid Lagoon in Qatar were investigated based on live observation as well as protargol- and silver nitrate-impregnated methods. The new species is characterised by a combination of features: the halophile habitat, a cell size of 50-65 × 33-40 μm, seven dorsal ridges, 10 commonly sized frontoventral cirri, two widely spaced marginal cirri, 10 dorsolateral kineties, and a double silverline pattern. The morphogenesis is similar to that of its congeners: (i) the oral primordium develops hypoapokinetally and the parental oral apparatus is retained; (ii) the frontoventral-transverse field of five streaks gives rise to the frontal, ventral, and transverse cirri, but not to the cirri I/1 and the marginal cirri; (iii) the dorsal somatic ciliature develops by intrakinetal proliferation of basal bodies in two anlagen per kinety that are just anterior and posterior to the future division furrow; (iv) the caudal cirri are formed by the two rightmost dorsolateral kineties. The SSU rDNA sequence of E. qatarensis branches with full support in the Euplotopsis elegans-Euplotes nobilii-Euplotopsis raikovi clade. The closest related publicly available SSU rDNA sequence is the one of E. nobilii, with which E. qatarensis has 93.4% sequence similarity. Euplotes parawoodruffi Song & Bradbury, 1997 is transferred to the genus Euplotoides based on the absence of frontoventral cirrus VI/3.
Collapse
Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, 7634 Doha, Qatar
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, D-67633, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Ecology, University of Kaiserslautern, D-67633, Kaiserslautern, Germany
| | - Jack W Fell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, 33149, USA
| | - Sabine Agatha
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, A-5020, Salzburg, Austria
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, 7634 Doha, Qatar
| | - Jiamei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 201306, Shanghai, China
| |
Collapse
|