This work is licensed under the Creative Commons Attribution 4.0 International License.
Ahmed, M., Back, M. A., Prior, T., Karssen, G., Lawson, R., Adams, I., and Sapp, M. 2019. Metabarcoding of soil nematodes: The importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s). Metabarcoding and Metagenomics 3:e36408. http://https://doi.org/10.3897/mbmg.3.36408AhmedM.BackM. A.PriorT.KarssenG.LawsonR.AdamsI.SappM.2019Metabarcoding of soil nematodes: The importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s)3e36408https://doi.org/10.3897/mbmg.3.36408Search in Google Scholar
Aitchison, J., Barceló-Vidal, C., Martín-Fernández, J. A., and Pawlowsky-Glahn, V. 2000. Logratio analysis and compositional distance. Mathematical Geology, 32(3):271–275. http://https://doi.org/10.1023/A:1007529726302AitchisonJ.Barceló-VidalC.Martín-FernándezJ. A.Pawlowsky-GlahnV.2000Logratio analysis and compositional distance323271–275https://doi.org/10.1023/A:1007529726302Search in Google Scholar
Alberts, J. S., Destouni, G., Duke-Sylvester, S. M., Magurran, A. E., Oberdorff, T., Reis, R. E., Winemiller, K. O., and Ripple, W. J. 2021. Scientists’ warning to humanity on the freshwater biodiversity crisis. Ambio 50:85–94. http://https://doi.org/10.1007/s13280-020-01318-8AlbertsJ. S.DestouniG.Duke-SylvesterS. M.MagurranA. E.OberdorffT.ReisR. E.WinemillerK. O.RippleW. J.2021Scientists’ warning to humanity on the freshwater biodiversity crisis5085–94https://doi.org/10.1007/s13280-020-01318-8Search in Google Scholar
Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., and Huse, S. M. 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA Genes. PLoS ONE 4:1–9. http://https://doi.org/10.1371/journal.pone.0006372Amaral-ZettlerL. A.McClimentE. A.DucklowH. W.HuseS. M.2009A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA Genes41–9https://doi.org/10.1371/journal.pone.0006372Search in Google Scholar
Aivelo, T. 2018. Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology http://145(5):608-621.https://doi.org/10.1017/S0031182017000610AiveloT.2018Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals1455608-621https://doi.org/10.1017/S0031182017000610Search in Google Scholar
Baker, E. A., and Woollard, A. 2019. How weird is the worm? Evolution of the developmental gene toolkit in Caenorhabditis elegans. Journal of Developmental Biology 7:19. http://https://doi.org/10.3390/jdb7040019BakerE. A.WoollardA.2019How weird is the worm? Evolution of the developmental gene toolkit in Caenorhabditis elegans719https://doi.org/10.3390/jdb7040019Search in Google Scholar
Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W., and Courchcamp, F. 2012. Impacts of climate change on the future of biodiversity. Ecology Letters 15:365– 377. http://https://doi.org/10.1111/j.1461-0248.2011.01736BellardC.BertelsmeierC.LeadleyP.ThuillerW.CourchcampF.2012Impacts of climate change on the future of biodiversity15365– 377https://doi.org/10.1111/j.1461-0248.2011.01736Search in Google Scholar
Bellard, C., Berney, C., and Leclerc, C. 2021. Looming extinctions due to invasive species: Irreversible loss of ecological strategy and evolutionary history. Global Change Biology 27:4967–4979. http://https://doi.org/10.1111/gcb.15771BellardC.BerneyC.LeclercC.2021Looming extinctions due to invasive species: Irreversible loss of ecological strategy and evolutionary history274967–4979https://doi.org/10.1111/gcb.15771Search in Google Scholar
Bezerra, T. N., Deprez, T., Eisendle, U., Hodda, M., Holovachov, O., Leduc, D., Mokievsky, V., Peña Santiago, R., Pérez-García, J. A., Sharma, J., Smol, N., Tchesunov, A., Vanreusel, A., Venekey, V., and Zhao, Z. 2022. Nemys, World Database of Nematodes. In O. Bánki, Y. Roskov, M. Döring, G. Ower, L. Vandepitte, D. Hobern, D. Remsen, P. Schalk, R. E. DeWalt, M. Keping, J. Miller, T. Orrell, R. Aalbu, R. Adlard, E. M. Adriaenssens, C. Aedo, E. Aescht, N. Akkari, P. Alfenas-Zerbini, et al., Catalogue of Life Checklist (ver. (04/2022)). http://https://doi.org/10.48580/dfpk-4rfBezerraT. N.DeprezT.EisendleU.HoddaM.HolovachovO.LeducD.MokievskyV.Peña SantiagoR.Pérez-GarcíaJ. A.SharmaJ.SmolN.TchesunovA.VanreuselA.VenekeyV.ZhaoZ.2022Nemys, World Database of NematodesInOBánkiYRoskovMDöringGOwerLVandepitteDHobernDRemsenPSchalkR. EDeWaltMKepingJMillerTOrrellRAalbuRAdlardE. MAdriaenssensCAedoEAeschtNAkkariPAlfenas-Zerbiniet alhttps://doi.org/10.48580/dfpk-4rfSearch in Google Scholar
Bodelier, P. L. E. 2011. Toward understanding, managing, and protecting microbial ecosystems. Frontiers in Microbiology 2:1–8. http://https://doi.org/10.3389/fmicb.2011.00080BodelierP. L. E.2011Toward understanding, managing, and protecting microbial ecosystems21–8https://doi.org/10.3389/fmicb.2011.00080Search in Google Scholar
Bonaglia, S., Nascimento, F. J. A., Bartoli, M., Klawonn, I., and Brüchert, V. 2014. Meiofauna increases bacterial denitrification in marine sediments. Nature Communications 5:1–9. http://https://doi.org/10.1038/NCOMMS6133BonagliaS.NascimentoF. J. A.BartoliM.KlawonnI.BrüchertV.2014Meiofauna increases bacterial denitrification in marine sediments51–9https://doi.org/10.1038/NCOMMS6133Search in Google Scholar
Bredtmann, C. M., Krücken, J., Murugaiyan, J., Kuzmina, T., and von Sanson-Himmelstjerna, G. 2017. Nematode species identification-current status, challenges, and future perspectives for cyathostomins. Frontiers in Cellular and Infection Microbiology 7:1–8. http://https://doi.org/10.3389/fcimb.2017.00283BredtmannC. M.KrückenJ.MurugaiyanJ.KuzminaT.von Sanson-HimmelstjernaG.2017Nematode species identification-current status, challenges, and future perspectives for cyathostomins71–8https://doi.org/10.3389/fcimb.2017.00283Search in Google Scholar
Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71-94. http://https://doi.org/10.1093/genetics/77.1.71BrennerS.19747771–94https://doi.org/10.1093/genetics/77.1.71Search in Google Scholar
Bubnoff, A. 2008. Next-generation sequencing: The race is on. Cell 132(5):721–3. http://https://doi.org/10.1016/j.cell.2008.02.028BubnoffA.2008Next-generation sequencing: The race is on1325721–3https://doi.org/10.1016/j.cell.2008.02.028Search in Google Scholar
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., and Holmes, S. P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13:581–583. http://https://doi.org/10.1038/nmeth.3869CallahanB. J.McMurdieP. J.RosenM. J.HanA. W.JohnsonA. J. A.HolmesS. P.2016DADA2: High-resolution sample inference from Illumina amplicon data13581–583https://doi.org/10.1038/nmeth.3869Search in Google Scholar
Cameron, E. K., Martins, I. S., Lavelle, P., Mathieu, J., Tedersoo, L., Bahram, M., Gottschall, F., Guerra, C. A., Hines, J., Patoine, G., Siebert, J., Winter, M., Cesarz, S., Ferlian, O., Kreft, H., Lovejoy, T. E., Montanarella, L., Orgiazzi, A., Periera, H. M., Phillips, H. R. P., Settele, J., Wall, D. H., and Eisenhauer, N. 2019. Global mismatches in aboveground and belowground biodiversity. Conservation Biology 33:1187–1192. http://https://doi.org/10.1111/cobi.13311CameronE. K.MartinsI. S.LavelleP.MathieuJ.TedersooL.BahramM.GottschallF.GuerraC. A.HinesJ.PatoineG.SiebertJ.WinterM.CesarzS.FerlianO.KreftH.LovejoyT. E.MontanarellaL.OrgiazziA.PerieraH. M.PhillipsH. R. P.SetteleJ.WallD. H.EisenhauerN.2019Global mismatches in aboveground and belowground biodiversity331187–1192https://doi.org/10.1111/cobi.13311Search in Google Scholar
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., Gormley N., Gilbert, J. A., Smith, G., and Knight, R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME Journal 6:1621– 1624. http://https://doi.org/10.1038/ismej.2012.8CaporasoJ. G.LauberC. L.WaltersW. A.Berg-LyonsD.HuntleyJ.FiererN.OwensS. M.BetleyJ.FraserL.BauerM.GormleyN.GilbertJ. A.SmithG.KnightR.2012Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms61621– 1624https://doi.org/10.1038/ismej.2012.8Search in Google Scholar
Colwell, R. R. 1997. Microbial diversity: the importance of exploration and conservation. Journal of Indian Microbiology and Biotechnology 18:302–307. http://https://doi.org/1 0.1038/sj.jim.2900390ColwellR. R.1997Microbial diversity: the importance of exploration and conservation18302–307https://doi.org/10.1038/sj.jim.2900390Search in Google Scholar
De Ley, P., and Blaxter, M. 2004. A new system for Nematoda: Combining morphological characters with molecular trees, and translating clades into ranks and taxa. Nematology Monographs and Perspectives 2:633– 653. http://https://doi.org/10.1163/9789004475236_061De LeyP.MBlaxter2004A new system for Nematoda: Combining morphological characters with molecular trees, and translating clades into ranks and taxa2633– 653https://doi.org/10.1163/9789004475236_061Search in Google Scholar
de Mesel, I., Derycke, S., Moens, T., van der Gucht, K., Vincx, M., and Swings, J. 2004. Top-down impact of bacterivorous nematodes on the bacterial community structure: A microcosm study. Environmental Microbiology 6:733–744. http://https://doi.org/10.1111/j.1462-2920.2004.00610.xIde MeselSDeryckeTMoensKvan der GuchtVincxM.SwingsJ.2004Top-down impact of bacterivorous nematodes on the bacterial community structure: A microcosm study6733–744https://doi.org/10.1111/j.1462-2920.2004.00610.xSearch in Google Scholar
Dixon, P. 2003. VEGAN, a package of R functions for community ecology. Journal of Vegetation Science 14:927–930. http://https://doi.org/10.1111/j.1654-1103.2003.tb02228.xDixonP.2003VEGAN, a package of R functions for community ecology14927–930https://doi.org/10.1111/j.1654-1103.2003.tb02228.xSearch in Google Scholar
Edgar, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797. http://https://doi.org/10.1093/nar/gkh340EdgarR. C.2004MUSCLE: Multiple sequence alignment with high accuracy and high throughput321792–1797https://doi.org/10.1093/nar/gkh340Search in Google Scholar
Gattoni, K., Gendron, E. M. S., Borgmeier, A., McQueen, J. P., Mullin, P. G., Powers, K., Powers, T. O., and Porazinska, D. L. 2022. Context-dependent role of abiotic and biotic factors structuring nematode communities along two environmental gradients. Molecular Ecology 00:1–14. http://https://doi.org/10.1111/mec.16541GattoniK.GendronE. M. S.BorgmeierA.McQueenJ. P.MullinP. G.PowersK.PowersT. O.PorazinskaD. L.2022Context-dependent role of abiotic and biotic factors structuring nematode communities along two environmental gradients001–14https://doi.org/10.1111/mec.16541Search in Google Scholar
Gebremikael, M. T., Steel, H., Buchan, D., Bert, W., and De Neve, S. 2016. Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions. Scientific Reports 6:1–10. http://https://doi.org/10.1038/srep32862GebremikaelM. T.SteelH.BuchanD.BertW.De NeveS.2016Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions61–10https://doi.org/10.1038/srep32862Search in Google Scholar
Geisen, S., Snoek, L. B., ten Hooven, F. C., Duyts, H., Kostenko, O., Bloem, J., Martens, H., Quist, C. W., Helder, J. A., and van der Putten, W. H. 2018. Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion. Methods in Ecology and Evolution 9(6):1366–1378. http://https://doi.org/10.1111/2041-210X.12999GeisenS.SnoekL. B.ten HoovenF. C.DuytsH.KostenkoO.BloemJ.MartensH.QuistC. W.HelderJ. A.van der PuttenW. H.2018Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion961366–1378https://doi.org/10.1111/2041-210X.12999Search in Google Scholar
Gerlach, S. A. 1978. Oecologia in stimulating bacterial productivity. Oecologia 69:55–69. http://https://doi.org/10.1007/BF00376996GerlachS. A.1978Oecologia in stimulating bacterial productivity6955–69https://doi.org/10.1007/BF00376996Search in Google Scholar
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., Del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H., Lara, E., Le Bescot, N., Logares, R., Mahé, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A. L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., and Christen, R. 2013. The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote small sub-unit. Nucleic Acids Research 41:D597–604. http://https://doi.org/10.1093/nar/gks1160GuillouL.BacharD.AudicS.BassD.BerneyC.BittnerL.BoutteC.BurgaudG.de VargasC.DecelleJ.Del CampoJ.DolanJ. R.DunthornM.EdvardsenB.HolzmannM.KooistraW. H.LaraE.Le BescotN.LogaresR.MahéF.MassanaR.MontresorM.MorardR.NotF.PawlowskiJ.ProbertI.SauvadetA. L.SianoR.StoeckT.VaulotD.ZimmermannP.ChristenR.2013The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote small sub-unit41D597–604https://doi.org/10.1093/nar/gks1160Search in Google Scholar
Heidemann, K., Hennies, A., Schakowske, J., Blumenberg, L., Ruess, L., Scheu, S., and Maraun, M. 2014. Free-living nematodes as prey for higher trophic levels of forest soil food webs. OIKOS 123:1199–1211. http://https://doi.org/10.1111/j.1600-0706.2013.00872.xHeidemannK.HenniesA.SchakowskeJ.BlumenbergL.RuessL.ScheuS.MaraunM.2014Free-living nematodes as prey for higher trophic levels of forest soil food webs1231199–1211https://doi.org/10.1111/j.1600-0706.2013.00872.xSearch in Google Scholar
Herren, G., Habraken, J., Waeyenberge, L., Haegeman, A., Viaene, N., Cougnon, M., Reheul, D., Steel, H., and Bert, W. 2020. Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots : A morphological and metabarcoding approach. PLOS ONE 15(3). http://https://doi.org/10.1371/journal.pone.0230153HerrenG.HabrakenJ.WaeyenbergeL.HaegemanA.ViaeneN.CougnonM.ReheulD.SteelH.BertW.2020Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots : A morphological and metabarcoding approach153https://doi.org/10.1371/journal.pone.0230153Search in Google Scholar
Hodda, M. E., Peters, L., and Traunspurger, W. 2009. Nematode diversity in terrestrial, freshwater aquatic and marine systems. Pp. 45–93 in M. J. Wilson, and T. Kakouli-Duarte, eds. Nematodes as environmental indicators. Wallingford, UK: CAB International.HoddaM. E.PetersL.TraunspurgerW.2009Nematode diversity in terrestrial, freshwater aquatic and marine systemsPp45–93inM. JWilsonTKakouli-DuarteWallingford, UKCAB InternationalSearch in Google Scholar
Hodda, M. 2022. Phylum Nematoda: a classification, catalogue and index of valid genera, with acensus of valid species. Zootaxa 5114(1):001–289. http://https://doi.org/10.11646/zootaxa.5114.1.1HoddaM.2022Phylum Nematoda: a classification, catalogue and index of valid genera, with acensus of valid species51141001–289https://doi.org/10.11646/zootaxa.5114.1.1Search in Google Scholar
Katoh, K., and Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30(4):772–780. http://https://doi.org/10.1093/molbev/mst010KatohK.StandleyD. M.2013MAFFT multiple sequence alignment software version 7: Improvements in performance and usability304772–780https://doi.org/10.1093/molbev/mst010Search in Google Scholar
Kiewnick, S., Holterman, M., van den Elsen, S., van Megen, H., Frey, J. E., and Helder, J. 2014. Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives. European Journal of Plant Pathology 140:97–110. http://https://doi.org/10.1007/s10658-014-0446-1KiewnickS.HoltermanM.van den ElsenS.van MegenH.FreyJ. E.HelderJ.2014Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives14097–110https://doi.org/10.1007/s10658-014-0446-1Search in Google Scholar
Koichiro, T., Glen, S., and Sudhir, K. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38:3022-3027.KoichiroT.GlenS.SudhirK.2021MEGA11: Molecular Evolutionary Genetics Analysis version 11383022–3027Search in Google Scholar
Macheriotou, L., Guilini, K., Bezerra, T. N., Tytgat, B., Nguyen, D. T., Phuong Nguyen, T. X., Noppe, F., Armenteros, M., Boufahja, F., Rigaux, A., Vanreusel, A., and Derycke, S. 2019. Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments. Ecology and Evolution 9(3):1211–1226. http://https://doi.org/10.1002/ece3.4814MacheriotouL.GuiliniK.BezerraT. N.TytgatB.NguyenD. T.Phuong NguyenT. X.NoppeF.ArmenterosM.BoufahjaF.RigauxA.VanreuselA.DeryckeS.2019Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments931211–1226https://doi.org/10.1002/ece3.4814Search in Google Scholar
Majdi, N., and Traunspurger, W. 2015. Free-living nematodes in the freshwater food web: A r e v i e w . Journal of Nematology 47:28–44.MajdiN.TraunspurgerW.2015Free-living nematodes in the freshwater food web: A r e v i e w4728–44Search in Google Scholar
Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal 17:10–12. http://https://doi.org/10.14806/ej.17.1.200MartinM.2011Cutadapt removes adapter sequences from high-throughput sequencing reads1710–12https://doi.org/10.14806/ej.17.1.200Search in Google Scholar
Müller, C. A., de Mattos Pereira, L., Lopes, C., Cares, J., dos Anjos Borges, L. G., Giongo, A., Graeff-Teixeira, C., and Morassutti, A. L. 2019. Meiofaunal diversity in the Atlantic Forest soil: A quest for nematodes in a native reserve using eukaryotic metabarcoding analysis. Forest Ecology and Management 453:117591. http://https://doi.org/10.1016/j.foreco.2019.117591MüllerC. A.de Mattos PereiraL.LopesC.CaresJ.dos Anjos BorgesL. G.GiongoA.Graeff-TeixeiraC.MorassuttiA. L.2019Meiofaunal diversity in the Atlantic Forest soil: A quest for nematodes in a native reserve using eukaryotic metabarcoding analysis453117591https://doi.org/10.1016/j.foreco.2019.117591Search in Google Scholar
Nascimento, F. J. A., Näslund, J., and Elmgren, N. 2012. Meiofauna enhances organic matter mineralization in soft sediment ecosystems. Limnology and Oceanography 57:338–346. http://https://doi.org/10.4319/lo.2012.57.1.0338NascimentoF. J. A.NäslundJ.ElmgrenN.2012Meiofauna enhances organic matter mineralization in soft sediment ecosystems57338–346https://doi.org/10.4319/lo.2012.57.1.0338Search in Google Scholar
Neher, D. A. 2010. Ecology of plant and free-living nematodes in natural and agricultural soil. Annual Review of Phytopathology 48:18.1–18.24. http://https://doi.org/10.1146/annurev-phyto-073009-114439NeherD. A.2010Ecology of plant and free-living nematodes in natural and agricultural soil4818.1–18.24https://doi.org/10.1146/annurev-phyto-073009-114439Search in Google Scholar
Nemys eds. (2022). Nemys: World Database of Nematodes. Accessed at http://https://nemys.ugent.be on 2022-11-28. doi:10.14284/366Nemys2022Accessed athttps://nemys.ugent.beon 2022-11-2810.14284/366Open DOISearch in Google Scholar
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., De Cáceres, M., Durand, S., Evangelista, H. B. A., FitzJohn, R., Friendly, M., Furneaux, B., Hannigan, G., Hill, M. O., Lahti, L., McGlinn, D., Ouellette, M. -H., Cunha, E. R., Smith, T., Stier, A., ter Braak, C. J. F., and Weedon, J. 2019. Vegan: Community ecology package. Available at: http://https://CRAN.R-project.org/package=veganOksanenJ.SimpsonG. L.BlanchetF. G.KindtR.LegendreP.MinchinP. R.O’HaraR. B.SolymosP.StevensM. H. H.SzoecsE.WagnerH.BarbourM.BedwardM.BolkerB.BorcardD.CarvalhoG.ChiricoM.De CáceresM.DurandS.EvangelistaH. B. A.FitzJohnR.FriendlyM.FurneauxB.HanniganG.HillM. O.LahtiL.McGlinnD.OuelletteM. -H.CunhaE. R.SmithT.StierA.ter BraakC. J. F.WeedonJ.2019Available athttps://CRAN.R-project.org/package=veganSearch in Google Scholar
Ottoni, J. R., dos Santos Grignet, R., Barros, M. G. A., Bernal, S. P. F., Panatta, A. A. S., Lacerda-Júnior, G. V., Centurion, V. B., Delforno, T. P., Goncalves, C. C. S., and Passarini, M. R. Z. 2022. DNA metabarcoding from microbial communities recovered from stream and its potential for bioremediation processes. Current Microbiology 79:69–70. http://https://doi.org/10.1007/s00284-021-02752-xOttoniJ. R.dos Santos GrignetR.BarrosM. G. A.BernalS. P. F.PanattaA. A. S.Lacerda-JúniorG. V.CenturionV. B.DelfornoT. P.GoncalvesC. C. S.PassariniM. R. Z.2022DNA metabarcoding from microbial communities recovered from stream and its potential for bioremediation processes7969–70https://doi.org/10.1007/s00284-021-02752-xSearch in Google Scholar
Pagan, C., Coyne, D., Carneiro, R., Kariuki, G., Luambana, N., Affokpon, A., and Williamson, V. M. 2015. Mitochondrial haplotype-based identification of ethanol-preserved root-knot nematodes from Africa. Phytopathology 105:350–357. http://https://doi.org/10.1094/PHYTO-08-14-0225-RPaganC.CoyneD.CarneiroR.KariukiG.LuambanaN.AffokponA.WilliamsonV. M.2015Mitochondrial haplotype-based identification of ethanol-preserved root-knot nematodes from Africa105350–357https://doi.org/10.1094/PHYTO-08-14-0225-RSearch in Google Scholar
Pascal, P. Y., Dupuy, C., Richard, P., Rzeznik-Orignac, J., and Niquil, N. 2008. Bacterivory of a mudflat nematode community under different environmental conditions. Marine Biology 154:671–682. http://https://doi.org/10.1007/s00227-008-0960-9PascalP. Y.DupuyC.RichardP.Rzeznik-OrignacJ.NiquilN.2008Bacterivory of a mudflat nematode community under different environmental conditions154671–682https://doi.org/10.1007/s00227-008-0960-9Search in Google Scholar
Porazinska, D. L., Giblin-Davis, R. M., Faller, L., Farmerie, W., Kanzaki, N., Morris, K., Powers, T. O., Tucker A. E., Sung W., and Thomas, W. K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resources 9:1439–1450. http://https://doi.org/10.1111/j.1755-0998.2009.02611.xPorazinskaD. L.Giblin-DavisR. M.FallerL.FarmerieW.KanzakiN.MorrisK.PowersT. O.TuckerA. E.SungW.ThomasW. K.2009Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity91439–1450https://doi.org/10.1111/j.1755-0998.2009.02611.xSearch in Google Scholar
Porazinska, D. L., Giblin-Davis, R. M., Sung, W., and Thomas, W. K. 2010. Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species. Zootaxa 2427:55–63. http://https://doi.org/10.11646/zootaxa.2427.1.6PorazinskaD. L.Giblin-DavisR. M.SungW.ThomasW. K.2010Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species242755–63https://doi.org/10.11646/zootaxa.2427.1.6Search in Google Scholar
Porazinska, D. L., Giblin-Davis, R. M., Powers, T. O., and Thomas, W. K. 2012. Nematode spatial and ecological patterns from tropical and temperate rainforests. PloS One 7:e44641. http://https://doi.org/10.1371/journal.pone.0044641PorazinskaD. L.Giblin-DavisR. M.PowersT. O.ThomasW. K.2012Nematode spatial and ecological patterns from tropical and temperate rainforests7e44641https://doi.org/10.1371/journal.pone.0044641Search in Google Scholar
Porazinska, D. L., Farrer, E. C., Spasojevic, M. J., Bueno De Mesquita, C. P., Sartwell, S. A., Smith, J. G., White, C. J., Suding, K. N., and Schmidt, S. K. 2018. Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem. Ecology 9:1942–1952. http://https://doi.org/10.1002/ecy.2420PorazinskaD. L.FarrerE. C.SpasojevicM. J.Bueno De MesquitaC. P.SartwellS. A.SmithJ. G.WhiteC. J.SudingK. N.SchmidtS. K.2018Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem91942–1952https://doi.org/10.1002/ecy.2420Search in Google Scholar
Porazinska, D. L., Bueno de Mesquita, C. P., Farrer, E. C., Spasojevic, M. J., Suding, K. N., and Schmidt, S. K. 2021. Nematode community diversity and function across an alpine landscape undergoing plant colonization of previously unvegetated soils. Soil Biology and Biochemistry 161:1–12. http://https://doi.org/10.1016/j.soilbio.2021.108380PorazinskaD. L.Bueno de MesquitaC. P.FarrerE. C.SpasojevicM. J.SudingK. N.SchmidtS. K.2021Nematode community diversity and function across an alpine landscape undergoing plant colonization of previously unvegetated soils1611–12https://doi.org/10.1016/j.soilbio.2021.108380Search in Google Scholar
Posa, M. R. C., Wijedada, L. L. S., and Corlett, R. T. 2011. Biodiversity and conservation of tropical peat swamp forests. BioScience http://61:49–57.https://doi.org/10.1525/bio.2011.61.1.10PosaM. R. C.WijedadaL. L. S.CorlettR. T.2011BioScience6149–57https://doi.org/10.1525/bio.2011.61.1.10Search in Google Scholar
Powers, T. O., and Harris, T. 1993. A polymerase chain reaction method for identification of five major Meloidogyne species. Journal of Nematology 25:1–6.PowersT. O.HarrisT.1993A polymerase chain reaction method for identification of five major Meloidogyne species251–6Search in Google Scholar
Powers, T. O., Harris, T. S., Higgins, R. S., Mullin, P. G., and Powers, K. S. 2017. An 18S rDNA perspective on the classification of Criconematoidea. Journal of Nematology 49(3): 236–244.PowersT. O.HarrisT. S.HigginsR. S.MullinP. G.PowersK. S.2017An 18S rDNA perspective on the classification of Criconematoidea493236–244Search in Google Scholar
Powers, T. O., Harris, T. S., Higgins, R. S., Mullin, P. G., and Powers, K. S. 2021. Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea. Genome 64:232–241. http://https://doi.org/10.1139/gen-2019-0196PowersT. O.HarrisT. S.HigginsR. S.MullinP. G.PowersK. S.2021Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea64232–241https://doi.org/10.1139/gen-2019-0196Search in Google Scholar
Price, M. N., Dehal, P. S., and Arkin, A. P. 2010. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490. http://https://doi.org/10.1371/journal.pone.0009490PriceM. N.DehalP. S.ArkinA. P.2010FastTree 2--approximately maximum-likelihood trees for large alignments53e9490https://doi.org/10.1371/journal.pone.0009490Search in Google Scholar
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O. 2013. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research 41:D590–D596. http://https://doi.org/10.1093/nar/gks1219QuastC.PruesseE.YilmazP.GerkenJ.SchweerT.YarzaP.PepliesJ.GlöcknerF. O.2013The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools41D590–D596https://doi.org/10.1093/nar/gks1219Search in Google Scholar
Santiago, A. D., Pereira, T. S., Mincks, S. L., and Bik, H. M. 2021. Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies. Environmental DNA 4:363–384. http://https://doi.org/10.1101/2021.06.16.448699SantiagoA. D.PereiraT. S.MincksS. L.BikH. M.2021Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies4363–384https://doi.org/10.1101/2021.06.16.448699Search in Google Scholar
Sapkota, R., and Nicolaisen, M. 2015. High-throughput sequencing of nematode communities from total soil DNA extractions. BMC Ecology 15:3. http://https://doi.org/10.1186/s12898-014-0034-4SapkotaR.NicolaisenM.2015High-throughput sequencing of nematode communities from total soil DNA extractions153https://doi.org/10.1186/s12898-014-0034-4Search in Google Scholar
Scheffers, B. R., De Meester, L., Bridge, T. C. L., Hoffmann, A. A., Pandolfi, J. M., Corlett, R. T., Butchart, S. H. M., Pearce-Kelly, P., Kovacs, K. M., Dudgeon, D., Pacifici, M., Rondinni, C., Foden, W. B., Martin, T. G., Mora, C., Bickford, D., and Watson, J. M. 2016. The broad footprint of climate change from genes to biomes to people. Science 354:6313. http://https://doi.org/10.1126/scienceScheffersB. R.De MeesterL.BridgeT. C. L.HoffmannA. A.PandolfiJ. M.CorlettR. T.ButchartS. H. M.Pearce-KellyP.KovacsK. M.DudgeonD.PacificiM.RondinniC.FodenW. B.MartinT. G.MoraC.BickfordD.WatsonJ. M.2016The broad footprint of climate change from genes to biomes to people3546313https://doi.org/10.1126/scienceSearch in Google Scholar
Schenk, J., Geisen, S., Kleinbölting, N., and Traunspurger, W. 2019. Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding Metagenomics 3:e46704. http://https://doi.org/10.3897/mbmg.3.46704SchenkJ.GeisenS.KleinböltingN.TraunspurgerW.2019Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth3e46704https://doi.org/10.3897/mbmg.3.46704Search in Google Scholar
Schratzberger, M., Holterman, M., van Oevelen, D., and Helder, J. 2019. A worm’s world: Ecological flexibility pays off for free-living nematodes in sediments and soils. BioScience 69:867–876. http://https://doi.org/10.1093/biosci/biz120SchratzbergerM.HoltermanM.van OevelenD.HelderJ.2019A worm’s world: Ecological flexibility pays off for free-living nematodes in sediments and soils69867–876https://doi.org/10.1093/biosci/biz120Search in Google Scholar
Sikder, M. M., Vestergård, M., Sapkota, R., Kyndt, T., and Nicolaisen, M. 2020. Evaluation of metabarcoding primers for analysis of soil nematode communities. Diversity 12(10):388. http://https://doi.org/10.3390/d12100388SikderM. M.VestergårdM.SapkotaR.KyndtT.NicolaisenM.2020Evaluation of metabarcoding primers for analysis of soil nematode communities1210388https://doi.org/10.3390/d12100388Search in Google Scholar
Sutherland, W. J., Freckleton, R. P., Godfray, C. J., Beissinger, S. R., Benton, T., Cameron, D. D., Carmel, Y., Coomes, D. A., Coulson, T., Emmerson, M. C., Hails, R. S., Hays, G. C., Hodgson D. J., Hutchings, M. J., Johnson, D., Jones, J. P. G., Keeling, M. J., Kokko, H., Kunin, W. E., Lambin, X., Lewis, O. T., Malhi, Y., Meiszkowska, N., Thompson, K., Travis, J. M. J., Turnbull, L. A., Wardle, D. A., and Wiegand, T. 2012. Identification of 100 fundamental ecological questions. Journal of Ecology 101:58–67. http://https://doi.org/10.1111/1365-2745.12025SutherlandW. J.FreckletonR. P.GodfrayC. J.BeissingerS. R.BentonT.CameronD. D.CarmelY.CoomesD. A.CoulsonT.EmmersonM. C.HailsR. S.HaysG. C.HodgsonD. J.HutchingsM. J.JohnsonD.JonesJ. P. G.KeelingM. J.KokkoH.KuninW. E.LambinX.LewisO. T.MalhiY.MeiszkowskaN.ThompsonK.TravisJ. M. J.TurnbullL. A.WardleD. A.WiegandT.2012Identification of 100 fundamental ecological questions10158–67https://doi.org/10.1111/1365-2745.12025Search in Google Scholar
Treonis, A. M., Unangst, S. K., Kepler, R. M., Buyer, J. S., Cavigelli, M. A., Mirsky, S. B., and Maul, J. E. 2018. Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches. Scientific Reports 8:2004. http://https://doi.org/10.1038/s41598-018-20366-5TreonisA. M.UnangstS. K.KeplerR. M.BuyerJ. S.CavigelliM. A.MirskyS. B.MaulJ. E.2018Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches82004https://doi.org/10.1038/s41598-018-20366-5Search in Google Scholar
Trevelline, B. K., Fontaine, S. S., Hartup, B. K., and Kohl, K. H. 2019. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proceeding of the Royal Society B: Biological Science 286:1–9. http://https://doi.org/10.1098/rspb.2018.2448TrevellineB. K.FontaineS. S.HartupB. K.KohlK. H.2019Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices2861–9https://doi.org/10.1098/rspb.2018.2448Search in Google Scholar
van den Hoogen, J., Geisen, S., Routh, D., Ferris, H., Traunspurger, W., Wardle, D. A., de Goede, R. G. M., Adams, B. J., Ahmad, W., Andriuzzi, W. S., Bardgett, R. D., Bonkowski, M., Campos-Herrera, R., Cares, J. E., Caruso, T., de Brito Caixeta, L., Chen, X., Costa, S. R., Creamer, R., Mauro da Cunha Castro, J., Dam, M., Djigal, D., Escuer, M., Griffiths, B. S., Gutiérrez, C., Hohberg, K., Kalinkina, D., Kardol, P., Kergunteuil, A., Korthals, G., Krashevska, V., Kudrin, A. A., Li, Q., Liang, W., Magilton, M., Marais, M., Martín, J. A. R., Matveeva, E., Mayad, E. H., Mulder, C., Mullin, P., Neilson, R., Nguyen, T. A. D., Nielsen, U. N., Okada, H., Rius, J. E. P., Pan, K., Peneva, V., Pellissier, L., Carlos Pereira da Silva, J., Pitteloud, C., Powers, T. O., Powers, K., Quist, C. W., Rasmann, S., Moreno, S. S., Scheu, S., Setälä, H., Sushchuk, A., Tiunov, A. V., Trap, J., van der Putten, W., Vestergård, M., Villenave, C., Waeyenberge, L., Wall, D. H., Wilschut, R., Wright, D. G., Yang, J., and Crowther, T. W. 2019. Soil nematode abundance and functional group composition at a global scale. Nature 572:194–198. http://https://doi.org/10.1038/s41586-019-1418-6Jvan den HoogenSGeisenDRouthHFerrisWTraunspurgerD. AWardleR. G. Mde GoedeB. JAdamsWAhmadW. SAndriuzziR. DBardgettMBonkowskiRCampos-HerreraJ. ECaresTCarusoLde Brito CaixetaXChenS. RCostaRCreamerJMauro da Cunha CastroMDamDDjigalMEscuerB. SGriffithsCGutiérrezKHohbergDKalinkinaPKardolAKergunteuilGKorthalsVKrashevskaA. AKudrinQLiWLiangMMagiltonMMaraisJ. A. RMartínEMatveevaE. HMayadCMulderPMullinRNeilsonT. A. DNguyenU. NNielsenHOkadaJ. E. PRiusKPanVPenevaLPellissierJCarlos Pereira da SilvaCPitteloudT. OPowersKPowersC. WQuistSRasmannS. SMorenoSScheuHSetäläASushchukA. VTiunovJTrapWvan der PuttenMVestergårdCVillenaveLWaeyenbergeD. HWallRWilschutD. GWrightJYangT. WCrowther2019Soil nematode abundance and functional group composition at a global scale572194–198https://doi.org/10.1038/s41586-019-1418-6Search in Google Scholar
van den Hoogen, J., Geisen, S., Wall, D. H., Wardle, D. A., Traunspurger, W., de Goede, R. G. M., Adams, B. J., Ahmad, W., Ferris, H., Bardgett, R. D., Bonkowski, M., Campos-Herrera, R., Cares, J. E., Caruso, T., de Brito Caixeta, L., Chen, X., Costa, S. R., Creamer, R., da Cunha e Castro, J. M., Dam, M., Djigal, D., Escuer, M., Griffiths, B. S., Gutiérrez, C., Hohberg, K., Kalinkina, D., Kardol, P., Kergunteuil, A., Korthals, G., Krashevska, V., Kudrin, A. A., Li, Q., Liang, W., Magilton, M., Marais, M., Martín, J. A. R., Matveeva, E., Mayad, E. H., Mzough, E., Mulder, C., Mullin, P., Neilson, R., Nguyen, T. A. D., Nielsen, U. N., Okada, H., Rius, J. E. P., Pan, K., Peneva, V., Pellissier, L., da Silva, J. C. P., Pitteloud, C., Powers, T. O., Powers, K., Quist, C. W., Rasmann, S., Moreno, S. S., Scheu, S., Setälä, H., Sushchuk, A., Tiunov, A. V., Trap, J., Vestergård, M., Villenave, C., Waeyenberge, L., Wilschut, R. A., Wright, D. G., Keith, A. M., Yang, J., Schmidt, O., Bouharroud, R., Ferji, Z., van der Putten, W. H., Routh, D., and Crowther, T. W. 2020. A global database of soil nematode abundance and functional group composition. Scientific Data 7:103. http://https://doi.org/10.1038/s41597-020-0437-3Jvan den HoogenSGeisenD. HWallD. AWardleWTraunspurgerR. G. Mde GoedeB. JAdamsWAhmadHFerrisR. DBardgettMBonkowskiRCampos-HerreraJ. ECaresTCarusoLde Brito CaixetaXChenS. RCostaRCreamerJ. Mda Cunha e CastroMDamDDjigalMEscuerB. SGriffithsCGutiérrezKHohbergDKalinkinaPKardolAKergunteuilGKorthalsVKrashevskaA. AKudrinQLiWLiangMMagiltonMMaraisJ. A. RMartínEMatveevaE. HMayadEMzoughCMulderPMullinRNeilsonT. A. DNguyenU. NNielsenHOkadaJ. E. PRiusKPanVPenevaLPellissierJ. C. Pda SilvaCPitteloudT. OPowersKPowersC. WQuistSRasmannS. SMorenoSScheuHSetäläASushchukA. VTiunovJTrapMVestergårdCVillenaveLWaeyenbergeR. AWilschutD. GWrightA. MKeithJYangOSchmidtRBouharroudZFerjiW. Hvan der PuttenDRouthT. WCrowther2020A global database of soil nematode abundance and functional group composition7103https://doi.org/10.1038/s41597-020-0437-3Search in Google Scholar
Vandepitte, L., Vanhoorne, B., Decock, W., Vranken, S., Lanssens, T., Dekeyzer, S., Verfaille, K., Horton, T., Kroh, A., Hernandez, F., and Mees, J. 2018. A decade of the World Register of Marine Species – General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue? PLOS ONE 13(4): e0194599. http://https://doi.org/10.1371/journal.pone.0194599VandepitteL.VanhoorneB.DecockW.VrankenS.LanssensT.DekeyzerS.VerfailleK.HortonT.KrohA.HernandezF.MeesJ.2018A decade of the World Register of Marine Species – General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue?134e0194599https://doi.org/10.1371/journal.pone.0194599Search in Google Scholar
Varmus, H. 2002. Genomic empowerment: the importance of public databases. Nature 32:3. http://https://doi.org/10.1038/ng963VarmusH.2002Genomic empowerment: the importance of public databases323https://doi.org/10.1038/ng963Search in Google Scholar
Waeyenberge, L., de Sutter, N., Viaene, N., and Haegeman, A. 2019. New insights into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities. Diversity 11(4):52. http://https://doi.org/10.3390/d11040052WaeyenbergeL.de SutterN.ViaeneN.HaegemanA.2019New insights into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities11452https://doi.org/10.3390/d11040052Search in Google Scholar
Wintle, B. A., Kujala, H., Whitehead, A., Cameron, A., Veloz, S., Kukkala, A., Moilanen, A., Gordon, A., Lentini, P. E., Cadenhead, N. C. R., and Bekessy, S. A. 2018. Global synthesis of conservation studies reveals the importance of small habitat patches for biodiversity. PNAS 116:909– 914. http://https://doi.org/10.1073/pnas.1813051115WintleB. A.KujalaH.WhiteheadA.CameronA.VelozS.KukkalaA.MoilanenA.GordonA.LentiniP. E.CadenheadN. C. R.BekessyS. A.2018Global synthesis of conservation studies reveals the importance of small habitat patches for biodiversity116909– 914https://doi.org/10.1073/pnas.1813051115Search in Google Scholar
Workentine, M. L., Chen, R., Zhu, S., Gavriliuc, S., Shaw, N., de Rijke, J., Reman, E. M., Avramenko, R. M., Wit, J., Poissant, J., and Gilleard, J. S. 2020. A database for ITS2 sequences from nematodes. BMC Genetics 21(74). http://https://doi.org/10.1186/s12863-020-00880-0WorkentineM. L.ChenR.ZhuS.GavriliucS.ShawN.de RijkeJ.RemanE. M.AvramenkoR. M.WitJ.PoissantJ.GilleardJ. S.2020A database for ITS2 sequences from nematodes2174https://doi.org/10.1186/s12863-020-00880-0Search in Google Scholar
WoRMS Editorial Board. 2022. World Register of Marine Species. http://https://doi.org/10.14284/170WoRMSEditorial Board.2022https://doi.org/10.14284/170Search in Google Scholar
Yeates, G. W., Bongers, T., de Goede, R. G. M., Freckman, D. W., and Georgieva, S. S. 199). Feeding habits in soil nematode families and genera-an outline for soil ecologists. Journal of Nematology, 25:315–331.YeatesG. W.BongersT.de GoedeR. G. M.FreckmanD. W.GeorgievaS. S.199)Feeding habits in soil nematode families and genera-an outline for soil ecologists25315–331Search in Google Scholar
Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J.,Ludwig, W., and Glöckner, F. O. 2014. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research 42:643–648. http://https://doi.org/10.1093/nar/gkt1209YilmazP.ParfreyL. W.YarzaP.GerkenJ.PruesseE.QuastC.SchweerT.PepliesJ.LudwigW.GlöcknerF. O.2014The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks42643–648https://doi.org/10.1093/nar/gkt1209Search in Google Scholar
Zepeda Mendoza, M. L., Sicheritz-Ponten, T., and Gilbert, M. T. P. 2015. Environmental genes and genomes: Understanding the differences and challenges in the approaches and software for their analyses. Briefings in Bioinformatics 16:745–758. http://https://doi.org/10.1093/bib/bbv001M. LZepeda MendozaTSicheritz-PontenM.T. PGilbert2015Environmental genes and genomes: Understanding the differences and challenges in the approaches and software for their analyses16745–758https://doi.org/10.1093/bib/bbv001Search in Google Scholar