REFERENCES
[dataset] Guerrieri, A., Bonin, A., Münkemüller, T., Gielly, L., Thuiller, W., Ficetola, G.F.; 2020; Raw and filtered supporting data for the study of soil preservation using environmental DNA; XXX
Bååth, E., & Arnebrant, K. (1994). Growth rate and response of bacterial communities to pH in limed and ash treated forest soils.Soil Biology and Biochemistry , 26 (8), 995–1001. doi: 10.1016/0038-0717(94)90114-7
Bálint, M., Bahram, M., Murat Eren, A., Faust, K., Fuhrman, J. A., Bj¨, B., … Tedersoo, L. (2016). Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiology Reviews , 017 , 686–700. doi: 10.1093/femsre/fuw017
Benjamini, Y., & Hochberg, Y. (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.Journal of the Royal Statistical Society: Series B (Methodological) , 57 (1), 289–300. doi: 10.1111/j.2517-6161.1995.tb02031.x
Borcard, D., Gillet, F., & Legendre, P. (2011). Numerical Ecology with R. In Numerical Ecology with R . doi: 10.1007/978-1-4419-7976-6
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., & Coissac, E. (2016). obitools: A unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources , 16 (1), 176–182. doi: 10.1111/1755-0998.12428
Brooks, M. E., Kristensen, K., van Benthem, K. J., Magnusson, A., Berg, C. W., Nielsen, A., … Bolker, B. M. (2017). glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R Journal , 9 (2), 378–400. doi: 10.32614/rj-2017-066
Brown, S. P., Veach, A. M., Rigdon-Huss, A. R., Grond, K., Lickteig, S. K., Lothamer, K., … Jumpponen, A. (2015). Scraping the bottom of the barrel: Are rare high throughput sequences artifacts? Fungal Ecology , 13 , 221–225. doi: 10.1016/j.funeco.2014.08.006
Calderón‐Sanou, I., Münkemüller, T., Boyer, F., Zinger, L., & Thuiller, W. (2020). From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? Journal of Biogeography , 47 (1), 193–206. doi: 10.1111/jbi.13681
Cantera, I., Cilleros, K., Valentini, A., Cerdan, A., Dejean, T., Iribar, A., … Brosse, S. (2019). Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers.Scientific Reports , 9 (1), 1–11. doi: 10.1038/s41598-019-39399-5
Cardona, S., Eck, A., Cassellas, M., Gallart, M., Alastrue, C., Dore, J., … Manichanh, C. (2012). Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiology ,12 . doi: 10.1186/1471-2180-12-158
Chase, M. W., & Hills, H. H. (1991). Silica gel: An ideal material for field preservation of leaf samples for DNA studies. TAXON ,40 (2), 215–220. doi: 10.2307/1222975
Chen, W., & Ficetola, G. F. (2020). Numerical methods for sedimentary‐ancient‐DNA‐based study on past biodiversity and ecosystem functioning. Environmental DNA , edn3.79. doi: 10.1002/edn3.79
CLARKE, K. R. (1993). Non-parametric multivariate analyses of changes in community structure. Austral Ecology , 18 (1), 117–143. doi: 10.1111/j.1442-9993.1993.tb00438.x
Coissac, E. (2012). OligoTag: A program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods in Molecular Biology , 888 , 13–31. doi: 10.1007/978-1-61779-870-2_2
Coissac, E., & Gonindard-Melodelima, C. (2019). Assessing the shared variation among high-dimensional data matrices: a modified version of the Procrustean correlation coefficient. BioRxiv Bioinformatics , 1–16. doi: 10.1101/842070
Consul, P. C., & Famoye, F. (1992). Generalized poisson regression model. Communications in Statistics - Theory and Methods ,21 (1), 89–109. doi: 10.1080/03610929208830766
De Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., … Velayoudon, D. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science , 348 (6237). doi: 10.1126/science.1261605
Delavaux, C. S., Bever, J. D., Karppinen, E. M., & Bainard, L. D. (2020). Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results. Ecology and Evolution , (November 2019), 1–13. doi: 10.1002/ece3.6219
Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E., Benavent-González, A., Eldridge, D. J., Bardgett, R. D., … Fierer, N. (2018). A global atlas of the dominant bacteria found in soil. Science , 359 (6373), 320–325. doi: 10.1126/science.aap9516
Dickie, I. A., Boyer, S., Buckley, H. L., Duncan, R. P., Gardner, P. P., Hogg, I. D., … Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA-based studies. Molecular Ecology Resources , 18 (5), 940–952. doi: 10.1111/1755-0998.12907
Drenovsky, R. E., Vo, D., Graham, K. J., & Scow, K. M. (2004). Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microbial Ecology ,48 (3), 424–430. doi: 10.1007/s00248-003-1063-2
Epp, L. S., Boessenkool, S., Bellemain, E. P., Haile, J., Esposito, A., Riaz, T., … Brochmann, C. (2012). New environmental metabarcodes for analysing soil DNA: Potential for studying past and present ecosystems. Molecular Ecology , 21 (8), 1821–1833. doi: 10.1111/j.1365-294X.2012.05537.x
Evans, S. E., Wallenstein, M. D., & Burke, I. C. (2014). Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought. Ecology , 95 (1), 110–122. doi: 10.1890/13-0500.1
Fernández-Calviño, D., & Bååth, E. (2010). Growth response of the bacterial community to pH in soils differing in pH. FEMS Microbiology Ecology , 73 (1), 149–156. doi: 10.1111/j.1574-6941.2010.00873.x
Ficetola, G. F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessière, J., … Pompanon, F. (2010). An In silico approach for the evaluation of DNA barcodes. BMC Genomics , 11 (1), 434. doi: 10.1186/1471-2164-11-434
Ficetola, G. F., Pansu, J., Bonin, A., Coissac, E., Giguet-Covex, C., De Barba, M., … Taberlet, P. (2015). Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources . doi: 10.1111/1755-0998.12338
Field, A., Miles, J., & Field, Z. (2012). Discovering statistics Using r . London: SAGE Publications.
Geyer, K. M., Altrichter, A. E., Takacs-Vesbach, C. D., Van Horn, D. J., Gooseff, M. N., & Barrett, J. E. (2014). Bacterial community composition of divergent soil habitats in a polar desert. FEMS Microbiology Ecology , 89 (2), 490–494. doi: 10.1111/1574-6941.12306
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., & Field, K. G. (1990). Genetic diversity in Sargasso Sea bacterioplankton.Nature , 345 (6270), 60–63. doi: 10.1038/345060a0
Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE ,10 (10), e0139633. doi: 10.1371/journal.pone.0139633
Guo, Y., Yang, G. Q., Chen, Y., Li, D., & Guo, Z. (2018). A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing. Plant Diversity ,40 (3), 106–116. doi: 10.1016/j.pld.2018.04.001
Hoffmann, C., Schubert, G., & Calvignac-Spencer, S. (2016, February 1). Aquatic biodiversity assessment for the lazy. Molecular Ecology , Vol. 25, pp. 846–848. doi: 10.1111/mec.13535
Huerlimann, R., Cooper, M. K., Edmunds, R. C., Villacorta-Rath, C., Le Port, A., Robson, H. L. A., … Jerry, D. R. (2020). Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non-environmental DNA specialists.Animal Conservation . doi: 10.1111/acv.12583
Ji, Y., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., … Yu, D. W. (2013). Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters ,16 (10), 1245–1257. doi: 10.1111/ele.12162
Kaiser, K., Wemheuer, B., Korolkow, V., Wemheuer, F., Nacke, H., Schöning, I., … Daniel, R. (2016). Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Scientific Reports , 6 (August), 1–12. doi: 10.1038/srep33696
Kumar, G., Eble, J. E., & Gaither, M. R. (2020). A practical guide to sample preservation and pre‐PCR processing of aquatic environmental DNA.Molecular Ecology Resources , 20 (1), 29–39. doi: 10.1111/1755-0998.13107
Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R., & Fierer, N. (2010). Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiology Letters , 307 (1), 80–86. doi: 10.1111/j.1574-6968.2010.01965.x
Legendre, P., & Borcard, D. (2018). Box-Cox-chord transformations for community composition data prior to beta diversity analysis.Ecography , 41 (11), 1820–1824. doi: 10.1111/ecog.03498
Legendre, P., & Legendre, L. (2012). Numerical Ecology . Amsterdam: Elsevier.
Majaneva, M., Diserud, O. H., Eagle, S. H. C., Boström, E., Hajibabaei, M., & Ekrem, T. (2018). Environmental DNA filtration techniques affect recovered biodiversity. Scientific Reports , 8 (1), 4682. doi: 10.1038/s41598-018-23052-8
Meisner, A., Jacquiod, S., Snoek, B. L., Ten Hooven, F. C., & van der Putten, W. H. (2018). Drought legacy effects on the composition of soil fungal and prokaryote communities. Frontiers in Microbiology ,9 (MAR), 294. doi: 10.3389/fmicb.2018.00294
Nichols, R. V., Vollmers, C., Newsom, L. A., Wang, Y., Heintzman, P. D., Leighton, M., … Shapiro, B. (2018). Minimizing polymerase biases in metabarcoding. Molecular Ecology Resources , 18 (5), 927–939. doi: 10.1111/1755-0998.12895
Ochoa-Hueso, R., Collins, S. L., Delgado-Baquerizo, M., Hamonts, K., Pockman, W. T., Sinsabaugh, R. L., … Power, S. A. (2018). Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents. Global Change Biology , 24 (7), 2818–2827. doi: 10.1111/gcb.14113
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., Mcglinn, D., … Maintainer, H. W. (2019). vegan: Community Ecology Package Version 2.5-6 . www.r-project.org
Orchard, S., Standish, R. J., Nicol, D., Dickie, I. A., & Ryan, M. H. (2017). Sample storage conditions alter colonisation structures of arbuscular mycorrhizal fungi and, particularly, fine root endophyte.Plant and Soil , 412 (1–2), 35–42. doi: 10.1007/s11104-016-2867-4
Paliy, O., & Shankar, V. (2016). Application of multivariate statistical techniques in microbial ecology. Molecular Ecology , Vol. 25, pp. 1032–1057. doi: 10.1111/mec.13536
Pettersson, M., & Bååth, E. (2003). Temperature-dependent changes in the soil bacterial community in limed and unlimed soil. FEMS Microbiology Ecology , 45 (1), 13–21. doi: 10.1016/S0168-6496(03)00106-5
R Core Team (2018). R: A Language and Environment for Statistical Computing . Vienna, Austria: R Foundation for Statistical Computing.
Strimmer, K. (2008). fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics (Oxford, England) , 24 (12), 1461–1462. doi: 10.1093/bioinformatics/btn209
Taberlet, P., Bonin, A., Zinger, L., & Coissac, É. (2018). Environmental DNA: For Biodiversity Research and Monitoring. InEnvironmental DNA: For Biodiversity Research and Monitoring . doi: 10.1093/oso/9780198767220.001.0001
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev, E. (2012). Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology , 21 (8), 2045–2050. doi: 10.1111/j.1365-294X.2012.05470.x
Ter Braak, C. J. F. (1986). Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis.Ecology , 67 (5), 1167–1179. doi: 10.2307/1938672
Ward, D. M., Weller, R., & Bateson, M. M. (1990). 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community.Nature , 345 (6270), 63–65. doi: 10.1038/345063a0
Zinger, L., Bonin, A., Alsos, I. G., Bálint, M., Bik, H., Boyer, F., … Taberlet, P. (2019a). DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions.Molecular Ecology , Vol. 28, pp. 1857–1862. doi: 10.1111/mec.15060
Zinger, L., Taberlet, P., Schimann, H., Bonin, A., Boyer, F., De Barba, M., … Chave, J. (2019b). Body size determines soil community assembly in a tropical forest. Molecular Ecology , 28 (3), 528–543. doi: 10.1111/mec.14919