Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities

被引:21
|
作者
Sikder, Md. Maniruzzaman [1 ,2 ]
Vestergard, Mette [1 ]
Sapkota, Rumakanta [3 ]
Kyndt, Tina [4 ]
Nicolaisen, Mogens [1 ]
机构
[1] Aarhus Univ, Dept Agroecol, Fac Tech Sci, DK-4200 Slagelse, Denmark
[2] Jahangirnagar Univ, Fac Biol Sci, Dept Bot, Dhaka 1342, Bangladesh
[3] Aarhus Univ, Dept Environm Sci, Fac Tech Sci, DK-4000 Roskilde, Denmark
[4] Univ Ghent, Dept Mol Biotechnol, Fac Biosci Engn, B-9000 Ghent, Belgium
来源
DIVERSITY-BASEL | 2020年 / 12卷 / 10期
关键词
nematode diversity; soil; rhizosphere; environmental; NGS; PLANT-PARASITIC NEMATODES; LIVING MARINE NEMATODES; RIBOSOMAL-RNA; DEEP-SEA; DNA; PHYLOGENY; DIVERSITY; PATTERNS; BARCODE; RDNA;
D O I
10.3390/d12100388
中图分类号
X176 [生物多样性保护];
学科分类号
090705 ;
摘要
While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step.
引用
收藏
页码:1 / 14
页数:14
相关论文
共 50 条
  • [1] Development and application of a DNA metabarcoding method for comprehensive analysis of soil nematode communities
    Kawanobe, Masanori
    Toyota, Koki
    Ritz, Karl
    [J]. APPLIED SOIL ECOLOGY, 2021, 166
  • [2] Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches
    Amy M. Treonis
    Samantha K. Unangst
    Ryan M. Kepler
    Jeffrey S. Buyer
    Michel A. Cavigelli
    Steven B. Mirsky
    Jude E. Maul
    [J]. Scientific Reports, 8
  • [3] Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches
    Treonis, Amy M.
    Unangst, Samantha K.
    Kepler, Ryan M.
    Buyer, Jeffrey S.
    Cavigelli, Michel A.
    Mirsky, Steven B.
    Maul, Jude E.
    [J]. SCIENTIFIC REPORTS, 2018, 8
  • [4] Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
    Kushida, Atsuhiko
    [J]. MICROBES AND ENVIRONMENTS, 2013, 28 (02) : 269 - 274
  • [5] Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary
    Kumar, Girish
    Reaume, Ashley M.
    Farrell, Emily
    Gaither, Michelle R.
    [J]. PLOS ONE, 2022, 17 (06):
  • [6] DNA metabarcoding of insects and allies: an evaluation of primers and pipelines
    Brandon-Mong, G. -J.
    Gan, H. -M.
    Sing, K. -W.
    Lee, P. -S.
    Lim, P. -E.
    Wilson, J. -J.
    [J]. BULLETIN OF ENTOMOLOGICAL RESEARCH, 2015, 105 (06) : 717 - 727
  • [7] A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish
    Zhang, Shan
    Zhao, Jindong
    Yao, Meng
    [J]. METHODS IN ECOLOGY AND EVOLUTION, 2020, 11 (12): : 1609 - 1625
  • [8] New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities
    Waeyenberge, Lieven
    de Sutter, Nancy
    Viaene, Nicole
    Haegeman, Annelies
    [J]. DIVERSITY-BASEL, 2019, 11 (04):
  • [9] Metabarcoding of nematode communities associated with Ananas comosus L. (Pineapple)
    Zurbano, Leilidyn Y.
    Deocaris, Chester C.
    Mapanao, Carmelita P.
    Rendon, Arnel O.
    Alvarez, Lourdes, V
    [J]. ASIAN JOURNAL OF AGRICULTURE AND BIOLOGY, 2023, 11 (03):
  • [10] Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities
    Schenk, Janina
    Kleinboelting, Nils
    Traunspurger, Walter
    [J]. ECOLOGY AND EVOLUTION, 2020, 10 (06): : 2885 - 2899