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Vafeiadou AM, Geldhof K, Barhdadi W, Baetens JM, De Baets B, Moens T, Daly AJ. Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex. PeerJ 2024; 12:e17324. [PMID: 38784398 PMCID: PMC11114120 DOI: 10.7717/peerj.17324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.
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Affiliation(s)
- Anna-Maria Vafeiadou
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Kevin Geldhof
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Wissam Barhdadi
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Jan M. Baetens
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Tom Moens
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Aisling J. Daly
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
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Senevirathna JDM, Yonezawa R, Saka T, Igarashi Y, Funasaka N, Yoshitake K, Kinoshita S, Asakawa S. Selection of a reference gene for studies on lipid-related aquatic adaptations of toothed whales ( Grampus griseus). Ecol Evol 2021; 11:17142-17159. [PMID: 34938499 PMCID: PMC8668803 DOI: 10.1002/ece3.8354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/06/2022] Open
Abstract
Toothed whales are one group of marine mammals that has developed special adaptations, such as echolocation for predation, to successfully live in a dynamic aquatic environment. Their fat metabolism may differ from that of other mammals because toothed whales have acoustic fats. Gene expression in the metabolic pathways of animals can change with respect to their evolution and environment. A real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for studying the relative expressions of genes. However, since the accuracy of RT-qPCR data is totally dependent on the reference gene, the selection of the reference gene is an essential step. In this study, 10 candidate reference genes (ZC3H10, FTL, LGALS1, RPL27, GAPDH, FTH1, DCN, TCTP, NDUS5, and UBIM) were initially tested for amplification efficiency using RT-qPCR. After excluding DCN, the remaining nine genes, which are nearly 100% efficient, were selected for the gene stability analysis. Stable reference genes across eight different fat tissue, liver, and muscle samples from Grampus griseus were identified by four algorithms, which were provided in Genorm, NormFinder, BestKeeper, and Delta CT. Finally, a RefFinder comprehensive ranking was performed based on the stability values, and the nine genes were ranked as follows: LGALS1 > FTL > GAPDH > ZC3H10 > FTH1 > NDUS5 > TCTP > RPL27 > UBIM. The LGALS1 and FTL genes were identified as the most stable novel reference genes. The third-ranked gene, GAPDH, is a well-known housekeeping gene for mammals. Ultimately, we suggest the use of LGALS1 as a reliable novel reference gene for genomics studies on the lipid-related aquatic adaptations of toothed whales.
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Affiliation(s)
- Jayan D. M. Senevirathna
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
- Department of Animal ScienceFaculty of Animal Science and Export AgricultureUva Wellassa UniversityBadullaSri Lanka
| | - Ryo Yonezawa
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Taiki Saka
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yoji Igarashi
- Department of Life Sciences and ChemistryGraduate School of BioresourcesMie UniversityMieJapan
| | - Noriko Funasaka
- Department of Life SciencesGraduate School of BioresourcesMie UniversityMieJapan
| | - Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shigeharu Kinoshita
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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Buys B, Derycke S, De Meester N, Moens T. Colonization of macroalgal deposits by estuarine nematodes through air and potential for rafting inside algal structures. PLoS One 2021; 16:e0246723. [PMID: 33857148 PMCID: PMC8049275 DOI: 10.1371/journal.pone.0246723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/25/2021] [Indexed: 11/19/2022] Open
Abstract
Dispersal is an important life-history trait. In marine meiofauna, and particularly in nematodes, dispersal is generally considered to be mainly passive, i.e. through transport with water currents and bedload transport. Because nematodes have no larval dispersal stage and have a poor swimming ability, their per capita dispersal capacity is expected to be limited. Nevertheless, many marine nematode genera and even species have near-cosmopolitan distributions, and at much smaller spatial scales, can rapidly colonise new habitat patches. Here we demonstrate that certain marine nematodes, like the morphospecies Litoditis marina, can live inside macroalgal structures such as receptacula and-to a lesser extent-floating bladders, which may allow them to raft over large distances with drifting macroalgae. We also demonstrate for the first time that these nematodes can colonize new habitat patches, such as newly deposited macroalgal wrack in the intertidal, not only through seawater but also through air. Our experimental set-up demonstrates that this aerial transport is probably the result of hitchhiking on vectors such as insects, which visit, and move between, the patches of deposited algae. Transport by wind, which has been observed for terrestrial nematodes and freshwater zooplankton, could not be demonstrated. These results can be important for our understanding of both large-scale geographic distribution patterns and of the small-scale colonization dynamics of habitat patches by marine nematodes.
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Affiliation(s)
- Bartelijntje Buys
- Department of Biology, Marine Biology Lab, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Department of Biology, Marine Biology Lab, Ghent University, Ghent, Belgium
- Center for Molecular Phylogeny and Evolution, Ghent University, Ghent, Belgium
| | - Nele De Meester
- Department of Biology, Marine Biology Lab, Ghent University, Ghent, Belgium
- Center for Molecular Phylogeny and Evolution, Ghent University, Ghent, Belgium
| | - Tom Moens
- Department of Biology, Marine Biology Lab, Ghent University, Ghent, Belgium
- * E-mail:
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Daly AJ, De Meester N, Baetens JM, Moens T, De Baets B. Untangling the mechanisms of cryptic species coexistence in a nematode community through individual‐based modelling. OIKOS 2021. [DOI: 10.1111/oik.07989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aisling J. Daly
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
| | - Nele De Meester
- Marine Biology Unit, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Jan M. Baetens
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
| | - Tom Moens
- Marine Biology Unit, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Bernard De Baets
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
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Nguyen PTX, Van Hoang H, Dinh HTK, Dorny P, Losson B, Bui DT, Lempereur L. Insights on foodborne zoonotic trematodes in freshwater snails in North and Central Vietnam. Parasitol Res 2021; 120:949-962. [PMID: 33426572 DOI: 10.1007/s00436-020-07027-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023]
Abstract
Foodborne zoonotic trematode (FZT) infections are common neglected tropical diseases in Southeast Asia. Their complicated life cycles involve freshwater snails as intermediate hosts. A cross-sectional study was conducted in Yen Bai and Thanh Hoa provinces in North and Central Vietnam, to investigate the diversity of cercariae of potential FZT and to construct the phylogenetic relationship of trematode cercariae based on the Internal Transcribed Spacer 2 (ITS2) region. Among 17 snail species collected from various habitats, 13 were infected by 10 cercarial groups among which parapleurolophocercous, pleurolophocercous, and echinostome cercariae were of zoonotic importance. The monophyletic tree separated cercarial sequences into different groups following the description of the cercariae families in which Haplorchidae, Opisthorchiidae, Echinochasmidae, and Echinostomatidae are important families of FZT. The overall prevalence was different among snail species and habitats and showed a seasonal trend. Parapleurolophocercous and echinostome cercariae emerged as the most common cercariae in snails in Yen Bai, while monostome, echinostome, and megalura cercariae were most common in Thanh Hoa. Using a molecular approach, we identified Parafossarulus striatulus as the first intermediate snail host of Clonorchis sinensis in Thac Ba Lake. Melanoides tuberculata and Bithynia fuchsiana were we identified preferred intermediate snail hosts of a diverse range of trematode species including intestinal flukes (i.e., Haplorchis pumilio and Echinochasmus japonicus) in Yen Bai and Thanh Hoa, respectively.
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Affiliation(s)
- Phuong Thi Xuan Nguyen
- Laboratory of Parasitology and Parasitic Diseases, Center for Fundamental and Applied Research for Animal and Health (FARAH), Faculty of Veterinary Medicine, ULiège, Boulevard de Colonster 20, 4000, Liège, Belgium.,Institute of Ecology and Biological Resources, Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
| | - Hien Van Hoang
- Institute of Ecology and Biological Resources, Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
| | - Huyen Thi Khanh Dinh
- Institute of Ecology and Biological Resources, Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
| | - Pierre Dorny
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerpen, Belgium
| | - Bertrand Losson
- Laboratory of Parasitology and Parasitic Diseases, Center for Fundamental and Applied Research for Animal and Health (FARAH), Faculty of Veterinary Medicine, ULiège, Boulevard de Colonster 20, 4000, Liège, Belgium
| | - Dung Thi Bui
- Institute of Ecology and Biological Resources, Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam.
| | - Laetitia Lempereur
- Laboratory of Parasitology and Parasitic Diseases, Center for Fundamental and Applied Research for Animal and Health (FARAH), Faculty of Veterinary Medicine, ULiège, Boulevard de Colonster 20, 4000, Liège, Belgium
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Macheriotou L, Guilini K, Bezerra TN, Tytgat B, Nguyen DT, Phuong Nguyen TX, Noppe F, Armenteros M, Boufahja F, Rigaux A, Vanreusel A, Derycke S. Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments. Ecol Evol 2019; 9:1211-1226. [PMID: 30805154 PMCID: PMC6374678 DOI: 10.1002/ece3.4814] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/24/2018] [Accepted: 11/25/2018] [Indexed: 11/30/2022] Open
Abstract
High-throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species-level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum-specific species-level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read-merging and two clustering algorithms and the cluster-free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus-level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species-level detections, which were, however, associated with higher error rates compared to ASVs. Genus-level assignments using ASVs exhibited higher accuracy and lower error rates compared to species-level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples.
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Affiliation(s)
- Lara Macheriotou
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Katja Guilini
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Tania Nara Bezerra
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Bjorn Tytgat
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Dinh Tu Nguyen
- Department of Nematology, Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Thi Xuan Phuong Nguyen
- Department of Nematology, Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Febe Noppe
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | | | - Fehmi Boufahja
- Laboratory of Biomonitoring of the Environment (LBE), Faculty of Sciences of BizerteUniversity of CarthageCarthageTunisia
| | - Annelien Rigaux
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Ann Vanreusel
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
| | - Sofie Derycke
- Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
- Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO)OostendeBelgium
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences (RBINS)BrusselBelgium
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7
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Guden RM, Vafeiadou AM, De Meester N, Derycke S, Moens T. Living apart-together: Microhabitat differentiation of cryptic nematode species in a saltmarsh habitat. PLoS One 2018; 13:e0204750. [PMID: 30261070 PMCID: PMC6160205 DOI: 10.1371/journal.pone.0204750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 09/13/2018] [Indexed: 11/26/2022] Open
Abstract
Coexistence of highly similar species is at odds with ecological theory of competition; coexistence, then, requires stabilizing mechanisms such as differences in ecological niche. In the bacterivore nematode Litoditis marina species complex, which occurs associated with macro-algae, four cryptic lineages (Pm I-IV) co-occur in the field along the south-western coast and estuaries of The Netherlands. Here we investigate the temporal and/or spatial niche differentiation in their natural environment using a qPCR-based detection and relative quantification method. We collected different algal species (i.e. two Fucus species and Ulva sp.) and separated algal structures (i.e. receptacula, thalli, non-fertile tips and bladders) at different sampling months and times (i.e. twice per sampling month), to examine differences in microhabitat use between coexisting L. marina species. Results demonstrate that the cryptic species composition varied among different algal species and algal structures, which was also subject to temporal shifts. Pm I dominated on Fucus spp., Pm II showed dominance on Ulva sp., while Pm III overall had the lowest frequencies. Microhabitat partitioning was most pronounced between the two cryptic species which had similar microbiomes (Pm I and Pm II), and less so between the two species which had significantly different microbiomes (Pm I and Pm III), suggesting that species which share the same microhabitats may avoid competition through resource partitioning. The interplay of microhabitat differentiation and temporal dynamics among the cryptic species of L. marina implies that there is a complex interaction between biotic components and abiotic factors which contributes to their coexistence in the field.
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Affiliation(s)
- Rodgee Mae Guden
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Mindanao State University- Iligan Institute of Technology, Iligan, Philippines
| | - Anna-Maria Vafeiadou
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Aristotle University of Thessaloniki, Biology Department, Thessaloniki, Greece
| | | | - Sofie Derycke
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Institute for Agricultural and Fisheries Research, Aquatic Environment and Quality, Oostende, Belgium
| | - Tom Moens
- Ghent University, Marine Biology Lab, Ghent, Belgium
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Blaxter M. Imagining Sisyphus happy: DNA barcoding and the unnamed majority. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0329. [PMID: 27481781 PMCID: PMC4971181 DOI: 10.1098/rstb.2015.0329] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 01/21/2023] Open
Abstract
The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on ‘charismatic megabionts’: larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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9
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Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition. Oecologia 2016; 182:559-71. [DOI: 10.1007/s00442-016-3677-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
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Grosemans T, Morris K, Thomas WK, Rigaux A, Moens T, Derycke S. Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species. Ecol Evol 2016; 6:1854-70. [PMID: 26933490 PMCID: PMC4760989 DOI: 10.1002/ece3.1975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/18/2015] [Accepted: 01/03/2016] [Indexed: 11/09/2022] Open
Abstract
Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.
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Affiliation(s)
- Tara Grosemans
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Krystalynne Morris
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - William Kelley Thomas
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - Annelien Rigaux
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; CeMoFe University of Ghent Karel Lodewijk Ledeganckstraat 359000 Gent Belgium
| | - Tom Moens
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Sofie Derycke
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; Royal Belgian Institute of Natural Sciences (RBINS) OD Taxonomy and Phylogeny Vautierstraat 291000 Brussels Belgium
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11
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Unraveling the intraguild competition between Oscheius spp. nematodes and entomopathogenic nematodes: Implications for their natural distribution in Swiss agricultural soils. J Invertebr Pathol 2015; 132:216-227. [PMID: 26519008 DOI: 10.1016/j.jip.2015.10.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/21/2015] [Accepted: 10/26/2015] [Indexed: 11/23/2022]
Abstract
Entomopathogenic nematodes (EPN) are excellent biological control agents to fight soil-dwelling insect pests. In a previous survey of agricultural soils of Switzerland, we found mixtures of free-living nematodes (FLN) in the genus Oscheius, which appeared to be in intense competition with EPN. As this may have important implications for the long-term persistence of EPN, we studied this intraguild competition in detail. We hypothesized that (i) Oscheius spp. isolates act as scavengers rather than entomopathogens, and (ii) cadavers with relatively small numbers of EPN are highly suitable resources for Oscheius spp. reproduction. To study this, we identified Oscheius spp. isolated from Swiss soils, quantified the outcome of EPN/Oscheius competition in laboratory experiments, developed species-specific primers and probe for quantitative real-time PCR, and evaluated their relative occurrence in the field in the context of the soil food web. Molecular analysis (ITS/D2D3) identified MG-67/MG-69 as Oscheius onirici and MG-68 as O. tipulae (Dolichura-group). Oscheius spp. indeed behaved as scavengers, reproducing in ∼64% of frozen-killed cadavers from controlled experiments. Mixed infection in the laboratory by Oscheius spp. with low (3 IJs) or high (20 IJs) initial EPN numbers revealed simultaneous reproduction in double-exposed cadavers which resulted in a substantial reduction in the number of EPN progeny from the cadaver. This effect depended on the number of EPN in the initial inoculum and differed by EPN species; Heterorhabditis megidis was better at overcoming competition. This study reveals Oscheius spp. as facultative kleptoparasites that compete with EPN for insect cadavers. Using real-time qPCR, we were able to accurately quantify this strong competition between FLN and EPN in cadavers that were recovered after soil baiting (∼86% cadavers with >50% FLN production). The severe competition within the host cadavers and the intense management of the soils in annual crops readily explain the low EPN numbers in Swiss field samples. The developed molecular tools can be used to elucidate the extent to which the competitive interactions affect EPN populations. This can help to develop strategies to achieve good persistence and natural EPN recycling, in particular in systems where native EPN levels are low, such as annual crops.
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12
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Daily Temperature Fluctuations Alter Interactions between Closely Related Species of Marine Nematodes. PLoS One 2015; 10:e0131625. [PMID: 26147103 PMCID: PMC4492701 DOI: 10.1371/journal.pone.0131625] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 01/15/2023] Open
Abstract
In addition to an increase in mean temperature, climate change models predict decreasing amplitudes of daily temperature fluctuations. In temperate regions, where daily and seasonal fluctuations are prominent, such decreases in daily temperature fluctuations can have a pronounced effect on the fitness of species and on the outcome of species interactions. In this study, the effect of a temperature regime with daily fluctuations versus a constant temperature on the fitness and interspecific interactions of three cryptic species of the marine nematode species complex of Litoditis marina (Pm I, Pm III and Pm IV) were investigated. In a lab experiment, different combinations of species (monospecific treatment: Pm I and Pm IV and Pm III alone; two-species treatment: Pm I + Pm IV; three-species treatment: Pm I + Pm IV + Pm III) were subjected to two different temperature regimes: one constant and one fluctuating temperature. Our results showed that fluctuating temperature had minor or no effects on the population fitness of the three species in monocultures. In contrast, interspecific interactions clearly influenced the fitness of all three species, both positively and negatively. Temperature regime did have a substantial effect on the interactions between the species. In the two-species treatment, temperature regime altered the interaction from a sort of mutualism to commensalism. In addition, the strength of the interspecific interactions changed depending on the temperature regime in the three-species treatment. This experiment confirms that interactions between the species can change depending on the abiotic environment; these results show that it is important to incorporate the effect of fluctuations on interspecific interactions to predict the effect of climate change on biodiversity.
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De Meester N, Derycke S, Rigaux A, Moens T. Active dispersal is differentially affected by inter- and intraspecific competition in closely related nematode species. OIKOS 2014. [DOI: 10.1111/oik.01779] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nele De Meester
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Sofie Derycke
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Annelien Rigaux
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Tom Moens
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
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First molecular phylogeny of the circumtropical bivalve family Pinnidae (Mollusca, Bivalvia): evidence for high levels of cryptic species diversity. Mol Phylogenet Evol 2014; 75:11-23. [PMID: 24569016 DOI: 10.1016/j.ympev.2014.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/05/2014] [Accepted: 02/13/2014] [Indexed: 11/22/2022]
Abstract
The family Pinnidae Leach, 1819, includes approximately 50 species of large subtidal and coastal marine bivalves. These commercially important species occur in tropical and temperate waters around the world and are most frequently found in seagrass meadows. The taxonomy of the family has been revised a number of times since the early 20th Century, the most recent revision recognizing 55 species distributed in three genera: Pinna, Atrina and Streptopinna, the latter being monotypic. However, to date no phylogenetic analysis of the family has been conducted using morphological or molecular data. The present study analyzed 306 pinnid specimens from around the world, comprising the three described genera and ca. 25 morphospecies. We sequenced the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear ribosomal genes 18S rRNA and 28S rRNA. Phylogenetic analysis of the data revealed monophyly of the genus Atrina but also that the genus Streptopinna is nested within Pinna. Based on the strong support for this relationship we propose a new status for Streptopinna Martens, 1880 and treat it as a subgenus (status nov.) of Pinna Linnaeus, 1758. The phylogeny and the species delimitation analyses suggest the presence of cryptic species in many morphospecies displaying a wide Indo-Pacific distribution, including Pinna muricata, Atrina assimilis, A. exusta and P. (Streptopinna) saccata but also in the Atlantic species A. rigida. Altogether our results highlight the challenges associated with morphological identifications in Pinnidae due to the presence of both phenotypic plasticity and morphological stasis and reveal that many pinnid species are not as widely distributed as previously thought.
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Vervoort MTW, Vonk JA, Mooijman PJW, Van den Elsen SJJ, Van Megen HHB, Veenhuizen P, Landeweert R, Bakker J, Mulder C, Helder J. SSU ribosomal DNA-based monitoring of nematode assemblages reveals distinct seasonal fluctuations within evolutionary heterogeneous feeding guilds. PLoS One 2012; 7:e47555. [PMID: 23112818 PMCID: PMC3480422 DOI: 10.1371/journal.pone.0047555] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 09/18/2012] [Indexed: 11/19/2022] Open
Abstract
Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.
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Affiliation(s)
- Mariëtte T. W. Vervoort
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
| | - J. Arie Vonk
- Laboratory for Ecological Risk Assessment, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Paul J. W. Mooijman
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
| | - Sven J. J. Van den Elsen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
| | - Hanny H. B. Van Megen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
| | - Peter Veenhuizen
- Laboratory for Soil and Crop Research (BLGG AgroXpertus), Wageningen, The Netherlands
| | - Renske Landeweert
- Laboratory for Soil and Crop Research (BLGG AgroXpertus), Wageningen, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
| | - Christian Mulder
- Laboratory for Ecological Risk Assessment, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University (WUR), Wageningen, The Netherlands
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De Meester N, Derycke S, Moens T. Differences in time until dispersal between cryptic species of a marine nematode species complex. PLoS One 2012; 7:e42674. [PMID: 22876328 PMCID: PMC3411683 DOI: 10.1371/journal.pone.0042674] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/11/2012] [Indexed: 12/02/2022] Open
Abstract
Co-occurrence of closely related species may be achieved in environments with fluctuating dynamics, where competitively inferior species can avoid competition through dispersal. Here we present an experiment in which we compared active dispersal abilities (time until first dispersal, number and gender of dispersive adults, and nematode densities at time of dispersal) in Litoditis marina, a common bacterivorous nematode species complex comprising four often co-occurring cryptic species, Pm I, II, III, and IV, as a function of salinity and food distribution. The experiment was conducted in microcosms consisting of an inoculation plate, connection tube, and dispersal plate. Results show species-specific dispersal abilities with Pm I dispersing almost one week later than Pm III. The number of dispersive adults at time of first dispersal was species-specific, with one dispersive female in Pm I and Pm III and a higher, gender-balanced, number in Pm II and Pm IV. Food distribution affected dispersal: in absence of food in the inoculation plate, all species dispersed after ca four days. When food was available Pm I dispersed later, and at the same time and densities irrespective of food conditions in the dispersal plate (food vs no food), suggesting density-dependent dispersal. Pm III dispersed faster and at a lower population density. Salinity affected dispersal, with slower dispersal at higher salinity. These results suggest that active dispersal in Litoditis marina is common, density-dependent, and with species, gender- and environment-specific dispersal abilities. These differences can lead to differential responses under suboptimal conditions and may help to explain temporary coexistence at local scales.
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Affiliation(s)
- Nele De Meester
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium.
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Campos-Herrera R, El-Borai FE, Duncan LW. Wide interguild relationships among entomopathogenic and free-living nematodes in soil as measured by real time qPCR. J Invertebr Pathol 2012; 111:126-35. [PMID: 22841945 DOI: 10.1016/j.jip.2012.07.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/10/2012] [Accepted: 07/15/2012] [Indexed: 10/28/2022]
Abstract
Entomopathogenic nematodes (EPNs) are promising biological control agents of soil-dwelling insect pests of many crops. These nematodes are ubiquitous in both natural and agricultural areas. Their efficacy against arthropods is affected directly and indirectly by food webs and edaphic conditions. It has long been suggested that a greater understanding of EPN ecology is needed to achieve consistent biological control by these nematodes and the development of molecular tools is helping to overcome obstacles to the study of cryptic organisms and complex interactions. Here we extend the repertoire of molecular tools to characterize soil food webs by describing primers/probe set to quantify certain free-living, bactivorous nematodes (FLBNs) that interact with EPNs in soil. Three FLBN isolates were recovered from soil baited with insect larvae. Morphological and molecular characterization confirmed their identities as Acrobeloides maximum (RT-1-R15C and RT-2-R25A) and Rhabditis rainai (PT-R14B). Laboratory experiments demonstrated the ability of these FLBNs to interfere with the development of Steinernema diaprepesi, Steinernema riobrave and Heterorhabditis indica parasitizing the weevil Diaprepes abbreviatus (P<0.001), perhaps due to resource competition. A molecular probe was developed for the strongest competitor, A. maximum. We selected the highly conserved SSU rDNA sequence to design the primers/probe, because these sequences are more abundantly available for free-living nematodes than ITS sequences that can likely provide better taxonomic resolution. Our molecular probe can identify organisms that share ⩾98% similarity at this locus. The use of this molecular probe to characterize soil communities from samples of nematode DNA collected within a citrus orchard revealed positive correlations (P<0.01) between Acrobeloides-group nematodes and total numbers of EPNs (S. diaprepesi, H. indica and Heterorhabditis zealandica) as well as a complex of nematophagous fungi comprising Catenaria sp. and Monachrosporium gephyropagum that are natural enemies of EPNs. These relationships can be broadly interpreted as supporting Linford's hypothesis, i.e., decomposition of organic matter (here, insect cadavers) greatly increases bactivorous nematodes and their natural enemies.
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Affiliation(s)
- Raquel Campos-Herrera
- Entomology and Nematology Department, University of Florida, Lake Alfred, FL 33850-2299, USA.
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