References
- Andrews S. (2010): FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Antich A., Palacin C., Wangensteen OS., Turon X. (2021): To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC bioinformatics, 22: 177. https://doi.org/10.1186/s12859-021-04115-6
- Bardgett R.D. & Van Der Putten W.H. (2014): Belowground biodiversity and ecosystem functioning. Nature, 515(7528): 505-511. https://doi.org/10.1038/nature13855
- Bogdanović D. (2014): Uzorkovanje zemljišta za ispitivanje plodnosti. In: Uzorkovanje zemljišta i biljaka za agrohemijske i pedološke analize (M. Manojlović, Ed.). Univerzitet u Novom Sadu, Poljoprivredni fakultet, Novi Sad, Srbija, pp.17-29.
- BOLD database (2024): BOLD Systems. Available at: https://www.boldsystems.org (accessed January 2024)
- Bolyen E., Rideout J.R., Dillon M.R., Bokulich N.A., Abnet C.C., Al-Ghalith G.A., Alexander H., Alm E.J., Arumugam M., Asnicar F. … Caporaso J.G. (2019): Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8): 852-857. https://doi.org/10.1038/s41587-019-0209-9
- 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. https://doi.org/10.1111/1755-0998.12428
- Brandt M.I., Trouche B., Quintric L., Günther B., Wincker P., Poulain J., Arnaud‐Haond S. (2021): Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding. Molecular Ecology Resources, 21(6): 1904-1921. https://doi.org/10.1111/1755-0998.13398
- Buchner D., Macher T.H., Leese F. (2022): APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. Bioinformatics, 38(20): 4817-4819. https://doi.org/10.1093/bioinformatics/btac588
- Buchner D. & Leese F. (2020): BOLDigger - a Python package to identify and organise sequences with the Barcode of Life Data systems. Metabarcoding and Metagenomics, 4: e53535. https://doi.org/10.3897/mbmg.4.53535
- Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P. (2016): DADA2: High-resolution sample inference from Illumina amplicon data. Nature methods, 13(7): 581-583. https://doi.org/10.1038/nmeth.3869
- Callahan B.J., McMurdie P.J., Holmes S.P. (2017): Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME journal, 11(12): 2639-2643. https://doi.org/10.1038/ismej.2017.119
- Clare E.L., Economou C.K., Bennett F.J., Dyer C.E., Adams K., McRobie B., Drinkwater R., Littlefair J.E. (2022): Measuring biodiversity from DNA in the air. Current Biology, 32(3): 693-700. https://doi.org/10.1016/j.cub.2021.11.064
- Cole J.R., Konstantinidis K., Farris R.J., Tiedje J.M. (2010): Microbial Diversity and Phylogeny: Extending from rRNAs to Genomes. In: Environmental Molecular Microbiology (W.Y. Liu and J.K. Jansson, Ed.). Caister Academic Press, United Kingdom, pp. 1-19.
- Dopheide A., Tooman L.K., Grosser S., Agabiti B., Rhode B., Xie D., Stevens M.I., Nelson N., Buckley T.R., Drummond A.J., Newcomb R.D. (2019): Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. Ecological Applications, 29(4): e01877. https://doi.org/10.1002/eap.1877
- Dopheide A., Makiola A., Orwin K.H., Holdaway R.J., Wood J.R., Dickie I.A. (2020): Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics. Elife, 9: e52787. https://doi.org/10.7554/eLife.52787
- Doran J.W & Zeiss M.R. (2000): Soil health and sustainability: managing the biotic component of soil quality. Applied soil ecology, 15(1): 3-11. https://doi.org/10.1016/S0929-1393(00)00067-6
- Elbrecht V. & Leese F. (2017): Validation and development of COI metabarcoding primers for freshwater macroinvertebrate bioassessment. Frontiers in Environmental Science, 5: 11. https://doi.org/10.3389/fenvs.2017.00011
- Elbrecht V. & Steinke D. (2019): Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring. Freshwater Biology, 64(2): 380-387. https://doi.org/10.1111/fwb.13220
- Ferris H. & Tuomisto H. (2015): Unearthing the role of biological diversity in soil health. Soil Biology and Biochemistry, 85: 101-109. https://doi.org/10.1111/fwb.13220
- Ferris H. & Tuomisto H. (2015): Unearthing the role of biological diversity in soil health. Soil Biology and Biochemistry, 85: 101-109. https://doi.org/10.1016/j.soilbio.2015.02.037
- Fitch A. (1863): Eighth report on the noxious and other insects of the State of New York. Transaction of the New York State Agricultural Society, 22: 657-691.
- Frøslev T.G., Kjøller R., Bruun H.H., Ejrnæs R., Brunbjerg A.K., Pietroni C., Hansen A.J. (2017): Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature communications, 8(1): 1188. https://doi.org/10.1038/s41467-017-01312-x
- Geisen S., Wall D.H., van der Putten W.H. (2019): Challenges and Opportunities for Soil Biodiversity in the Anthropocene. Current Biology, 29(19): 1036-1044. https://doi.org/10.1016/j.cub.2019.08.007
- Guerrieri A., Bonin A., Münkemüller T., Gielly L., Thuiller W., Francesco Ficetola G. (2021): Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology, 30(13): 3313-3325. https://doi.org/10.1111/mec.15674
- Hebert P.D., Cywinska A., Ball S.L., DeWaard J.R. (2003): Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512): 313-321. https://doi.org/10.1098/rspb.2002.2218
- Hermans S.M, Lear G., Buckley T.R, Buckle H.L. (2022): Environmental DNA sampling detects between-habitat variation in soil arthropod communities, but is a poor indicator of fine-scale spatial and seasonal variation. Ecological Indicators, 140: 109040. https://doi.org/10.1016/j.ecolind.2022.109040
- Kirse A., Bourlat S.J., Langen K., Fonseca V.G. (2021): Unearthing the potential of soil eDNA metabarcoding - Towards best practice advice for invertebrate biodiversity assessment. Frontiers in Ecology and Evolution, 9: 630560. https://doi.org/10.3389/fevo.2021.630560
- Macher J-N., Vivancos A., Piggott J.J., Centeno F.C., Matthaei C.D., Leese F. (2018): Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers. Molecular Ecology Resources, 18(6): 1456-1468. https://doi.org/10.1111/1755-0998.12940
- Macher T.H., Beermann A.J., Leese F. (2021): TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data. Molecular Ecology Resources, 21(5): 1705-1714. https://doi.org/10.1111/1755-0998.13358
- Martin M. (2011): Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1): 10-12. https://doi.org/10.14806/ej.17.1.200
- McClenaghan B., Fahner N., Cote D., Chawarski J., McCarthy A., Rajabi H., Singer G., Hajibabaei M. (2020) Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes. PLoS One, 15(11): e0236540. https://doi.org/10.1371/journal.pone.0236540
- Michaelsen W. (1891): Oligochaeten des Naturhistorischen Museums in Hamburg IV. Jahrbuch der Hamburgischen Wissen- schaftlichen Anstalten, 8: 1-42.
- Nejgebauer V., Živković B., Tanasijević Đ., Milјković N. (1971): Pedološka karta Vojvodine R 1:50.000, Institut za polјoprivredna istraživanja, Novi Sad, Srbija.
- Pavlović P., Kostić N., Karadžić B., Mitrović, M. (2017): The soils of Serbia. Springer Netherlands. 1-225. 10.1007/978-94-017-8660-7
- Ponge J.F., Pérès G., Guernion M., Ruiz-Camacho N., Cortet J., Pernin C., Villenave C., Chaussod R., Martin-Laurent F., Bispo A., Cluzeau D. (2013): The impact of agricultural practices on soil biota: a regional study. Soil Biology and Biochemistry, 67: 271-284. https://doi.org/10.1016/j.soilbio.2013.08.026
- Porter T.M., Morris D.M., Basiliko N., Hajibabaei M., Doucet D., Bowman S., Emilson E.J.S., Emilson C.E., Chartrand D., Wainio-Keizer K., Séguin A., Venier L. (2019): Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators. Scientific Reports, 9(1): 18218. https://doi.org/10.1038/s41598-019-54532-0
- Prakash S. & Verma A.K. (2022): Anthropogenic activities and Biodiversity threats. International Journal of Biological Innovations IJBI, 4(1): 94-103. https://doi.org/10.46505/IJBI.2022.4110
- Rota N., Canedoli C., Ferrè C., Ficetola G.F., Guerrieri A., Padoa-Schioppa E. (2020): Evaluation of soil biodiversity in alpine habitats through eDNA metabarcoding and relationships with environmental features. Forests, 11(7): 738. https://doi.org/10.3390/f11070738
- Rognes T., Flouri T., Nichols B., Quince C., Mahé F. (2016): VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4: e2584. 10.7717/peerj.2584
- Škorić A., Filipovski G., Ćirić M. (1985): Klasifikacija zemlјišta Jugoslavije, Akademija nauka i umjetnosti Bosne i Hercegovine, Posebna izdanja, knjiga LXXVIII, Sarajevo.
- Taberlet P., Coissac E., Hajibabaei M., Rieseberg L.H. (2012a): Environmental DNA. Molecular Ecology, 21(8): 1789-1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x
- Taberlet P., Coissac E., Pompanon F., Brochmann C., Willerslev E. (2012b): Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21(8): 2045-2050. https://doi.org/10.1111/j.1365-294X.2012.05470.x
- Turbé A., De Toni A., Benito P., Lavelle P., Lavelle P., Camacho N.R., Van der Putten W.H., Labouze E., Mudgal S. (2010): Soil biodiversity: functions, threats and tools for policy makers. Bio Intelligence Service, IRD, and NIOO, Report for European Commission (DG Environment). Available at: https://hal-bioemco.ccsd.cnrs.fr/bioemco-00560420
- Vasin J., Sekulić P., Milić S., Nešić L., Belić M., Ninkov J., & Zeremski, T. (2013): Pedogenesis of Solonchak soils in Northern Vojvodina. The 1st International Congress on Soil Science, XIII National Congress in Soil Science. Soil Science Society of Serbia and Soil Science Institute. Belgrade, Serbia, 23-26 September, 13.
- Watts C., Dopheide A., Holdaway R., Davis C., Wood J., Thornburrow D., Dickie I.A. (2019) DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques. Austral Entomology, 58(3): 675-686. https://doi.org/10.1111/aen.12384
- Weigand H., Beermann A.J., Čiampor F., Costa F.O., Csabai Z., Duarte S., Geiger M.F., Grabowski M., Rimet F., Rulik B. … Ekrem T. (2019): DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of the Total Environment, 678: 499-524. https://doi.org/10.1016/j.scitotenv.2019.04.247
- Zepeda Mendoza M.L., Sicheritz-Ponten T., 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(5): 745-758. https://doi.org/10.1093/bib/bbv001
- Zeremski T., Tomić N., Milić S., Vasin J., Schaetzl R.J., Milić D., Gavrilov M.B., Živanov M.,, Ninkov J., Marković S.B. (2021): Saline soils: a potentially significant geoheritage of the Vojvodina region, Northern Serbia. Sustainability, 13(14): 7891. https://doi.org/10.3390/su13147891
