메뉴 건너뛰기




Volumn 7, Issue 9, 2016, Pages 1071-1081

Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

Author keywords

Acari; biomonitoring; Collembola; community structure; deep soil; high throughput sequencing; mesofauna extraction; metagenome skimming; phylodiversity; soil biodiversity

Indexed keywords


EID: 84963655955     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12557     Document Type: Article
Times cited : (78)

References (47)
  • 4
    • 0036997442 scopus 로고    scopus 로고
    • Causes and consequences of biological diversity in soil
    • Bardgett, R.D. (2002) Causes and consequences of biological diversity in soil. Zoology, 105, 367–374.
    • (2002) Zoology , vol.105 , pp. 367-374
    • Bardgett, R.D.1
  • 5
    • 84923094743 scopus 로고    scopus 로고
    • Belowground biodiversity and ecosystem functioning
    • Bardgett, R.D. & van der Putten, W.H. (2014) Belowground biodiversity and ecosystem functioning. Nature, 515, 505–511.
    • (2014) Nature , vol.515 , pp. 505-511
    • Bardgett, R.D.1    van der Putten, W.H.2
  • 7
    • 25444472044 scopus 로고    scopus 로고
    • transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
    • Bininda-Emonds, O.R.P. (2005) transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics, 6, 156.
    • (2005) BMC Bioinformatics , vol.6 , pp. 156
    • Bininda-Emonds, O.R.P.1
  • 9
    • 84886097822 scopus 로고    scopus 로고
    • Collembola, the biological species concept and the underestimation of global species richness
    • Cicconardi, F., Fanciulli, P. & Emerson, B. (2013) Collembola, the biological species concept and the underestimation of global species richness. Molecular Ecology, 2, 5382–5396.
    • (2013) Molecular Ecology , vol.2 , pp. 5382-5396
    • Cicconardi, F.1    Fanciulli, P.2    Emerson, B.3
  • 10
    • 73949143351 scopus 로고    scopus 로고
    • Deep phylogeographic divisions and long-term persistence of forest invertebrates (Hexapoda: Collembola) in the North-Western Mediterranean basin
    • Cicconardi, F., Nardi, F., Emerson, B., Frati, F. & Fanciulli, P. (2010) Deep phylogeographic divisions and long-term persistence of forest invertebrates (Hexapoda: Collembola) in the North-Western Mediterranean basin. Molecular Ecology, 19, 386–400.
    • (2010) Molecular Ecology , vol.19 , pp. 386-400
    • Cicconardi, F.1    Nardi, F.2    Emerson, B.3    Frati, F.4    Fanciulli, P.5
  • 12
    • 77954233818 scopus 로고    scopus 로고
    • Macroecological patterns in soil communities
    • Decaëns, T. (2010) Macroecological patterns in soil communities. Global Ecology and Biogeography, 19, 287–302.
    • (2010) Global Ecology and Biogeography , vol.19 , pp. 287-302
    • Decaëns, T.1
  • 14
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics (Oxford, England), 26, 2460–2461.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 15
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: highly accurate OTU sequences from microbial amplicon reads
    • Edgar, R.C. (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996–998.
    • (2013) Nature Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 16
    • 84860881754 scopus 로고    scopus 로고
    • Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida)
    • Erdmann, G., Scheu, S. & Maraun, M. (2012) Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida). Experimental & Applied Acarology, 57, 157–169.
    • (2012) Experimental & Applied Acarology , vol.57 , pp. 157-169
    • Erdmann, G.1    Scheu, S.2    Maraun, M.3
  • 19
    • 84930383193 scopus 로고    scopus 로고
    • Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods
    • Flynn, J.M., Brown, E.A., Chain, F.J.J., MacIsaac, H.J. & Cristescu, M.E. (2015) Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecology and Evolution, 5, 2252–2266.
    • (2015) Ecology and Evolution , vol.5 , pp. 2252-2266
    • Flynn, J.M.1    Brown, E.A.2    Chain, F.J.J.3    MacIsaac, H.J.4    Cristescu, M.E.5
  • 20
    • 0028528103 scopus 로고
    • DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates
    • Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299.
    • (1994) Molecular Marine Biology and Biotechnology , vol.3 , pp. 294-299
    • Folmer, O.1    Black, M.2    Hoeh, W.3    Lutz, R.4    Vrijenhoek, R.5
  • 24
    • 33646201598 scopus 로고    scopus 로고
    • Molecular sequencing and morphological analysis of a nematode community
    • Griffiths, B.S., Donn, S., Neilson, R. & Daniell, T.J. (2006) Molecular sequencing and morphological analysis of a nematode community. Applied Soil Ecology, 32, 325–337.
    • (2006) Applied Soil Ecology , vol.32 , pp. 325-337
    • Griffiths, B.S.1    Donn, S.2    Neilson, R.3    Daniell, T.J.4
  • 25
    • 79952001955 scopus 로고    scopus 로고
    • Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
    • Hao, X., Jiang, R. & Chen, T. (2011) Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics, 27, 611–618.
    • (2011) Bioinformatics , vol.27 , pp. 611-618
    • Hao, X.1    Jiang, R.2    Chen, T.3
  • 28
    • 84883816660 scopus 로고    scopus 로고
    • Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
    • Ji, Y., Ashton, L., Pedley, S.M., Edwards, D.P., Tang, Y., Nakamura, A. et al. (2013) Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters, 16, 1245–1257.
    • (2013) Ecology Letters , vol.16 , pp. 1245-1257
    • Ji, Y.1    Ashton, L.2    Pedley, S.M.3    Edwards, D.P.4    Tang, Y.5    Nakamura, A.6
  • 29
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–3066.
    • (2002) Nucleic Acids Research , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 30
    • 84987772826 scopus 로고    scopus 로고
    • Techniques: tamisages, lavages et autres berlèses
    • Lemagnen, R. (2009) Techniques: tamisages, lavages et autres berlèses. Invertébrés Armoricains, 1, 19–22.
    • (2009) Invertébrés Armoricains , vol.1 , pp. 19-22
    • Lemagnen, R.1
  • 31
    • 84864483625 scopus 로고    scopus 로고
    • RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
    • Lohse, M., Bolger, A. & Nagel, A. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40, W622–W627.
    • (2012) Nucleic Acids Research , vol.40 , pp. W622-W627
    • Lohse, M.1    Bolger, A.2    Nagel, A.3
  • 32
    • 84907710189 scopus 로고    scopus 로고
    • Swarm: robust and fast clustering method for amplicon-based studies
    • Mahé, F., Rognes, T., Quince, C., de Vargas, C. & Dunthorn, M. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ, 2, e593.
    • (2014) PeerJ , vol.2
    • Mahé, F.1    Rognes, T.2    Quince, C.3    de Vargas, C.4    Dunthorn, M.5
  • 33
    • 84987706968 scopus 로고
    • Description d'un nouveau procedé de capture des Coléoptères hypogés
    • Normand, D.H. (1909) Description d'un nouveau procedé de capture des Coléoptères hypogés. Bulletin de la Société entomologique de France, 19, 329.
    • (1909) Bulletin de la Société entomologique de France , vol.19 , pp. 329
    • Normand, D.H.1
  • 35
    • 0034484104 scopus 로고    scopus 로고
    • Vertical distribution of Collembola (Hexapoda) and their food resources in organic horizons of beech forests
    • Ponge, J. (2000) Vertical distribution of Collembola (Hexapoda) and their food resources in organic horizons of beech forests. Biology and Fertility of Soils, 32, 508–522.
    • (2000) Biology and Fertility of Soils , vol.32 , pp. 508-522
    • Ponge, J.1
  • 36
    • 84873295621 scopus 로고    scopus 로고
    • Plant–soil feedbacks mediated by humus forms: a review
    • Ponge, J.-F. (2013) Plant–soil feedbacks mediated by humus forms: a review. Soil Biology and Biochemistry, 57, 1048–1060.
    • (2013) Soil Biology and Biochemistry , vol.57 , pp. 1048-1060
    • Ponge, J.-F.1
  • 37
    • 84874575602 scopus 로고    scopus 로고
    • PyroClean: denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation
    • Ramirez-Gonzalez, R., Yu, D.W., Bruce, C., Heavens, D., Caccamo, M. & Emerson, B.C. (2013) PyroClean: denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation. PLoS One, 8, e57615.
    • (2013) PLoS One , vol.8
    • Ramirez-Gonzalez, R.1    Yu, D.W.2    Bruce, C.3    Heavens, D.4    Caccamo, M.5    Emerson, B.C.6
  • 38
    • 79959651994 scopus 로고    scopus 로고
    • Eficiencia del embudo Berlese-Tullgren para extracción de artrópodos edáficos en suelos argiudoles típicos de la provincia de Buenos Aires
    • Sandler, R., Falco, L., Ciocco, C.Di., de Luca, R. & Coviella, C.E. (2010) Eficiencia del embudo Berlese-Tullgren para extracción de artrópodos edáficos en suelos argiudoles típicos de la provincia de Buenos Aires. CI. Suelo (Argentina), 28, 1–7.
    • (2010) CI. Suelo (Argentina) , vol.28 , pp. 1-7
    • Sandler, R.1    Falco, L.2    Ciocco, C.D.3    de Luca, R.4    Coviella, C.E.5
  • 39
    • 84943579883 scopus 로고    scopus 로고
    • Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies
    • Schnell, I.B., Bohmann, K. & Gilbert, M.T.P. (2015) Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources, 15, 883–894.
    • (2015) Molecular Ecology Resources , vol.15 , pp. 883-894
    • Schnell, I.B.1    Bohmann, K.2    Gilbert, M.T.P.3
  • 40
    • 84987710782 scopus 로고    scopus 로고
    • Updating taxonomic biogeography in the light of new methods–examples from Collembola
    • Shaw, P., Faria, C. & Emerson, B. (2013) Updating taxonomic biogeography in the light of new methods–examples from Collembola. Soil Organisms, 85, 161–170.
    • (2013) Soil Organisms , vol.85 , pp. 161-170
    • Shaw, P.1    Faria, C.2    Emerson, B.3
  • 43
    • 84941808021 scopus 로고    scopus 로고
    • High-throughput monitoring of wild bee diversity and abundance via mitogenomics (M Gilbert, Ed.)
    • Tang, M., Hardman, C.J., Ji, Y., Meng, G., Liu, S., Tan, M. et al. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics (M Gilbert, Ed.). Methods in Ecology and Evolution, 6, 1034–1043.
    • (2015) Methods in Ecology and Evolution , vol.6 , pp. 1034-1043
    • Tang, M.1    Hardman, C.J.2    Ji, Y.3    Meng, G.4    Liu, S.5    Tan, M.6
  • 45
    • 84872337761 scopus 로고    scopus 로고
    • Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity
    • Yang, C., Ji, Y., Wang, X., Yang, C. & Yu, D.W. (2013) Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity. Science China. Life Sciences, 56, 73–81.
    • (2013) Science China. Life Sciences , vol.56 , pp. 73-81
    • Yang, C.1    Ji, Y.2    Wang, X.3    Yang, C.4    Yu, D.W.5
  • 46
    • 84905002043 scopus 로고    scopus 로고
    • Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator
    • Yang, C., Wang, X., Miller, J.A., de Blécourt, M., Ji, Y., Yang, C., Harrison, R.D. & Yu, D.W. (2014) Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator. Ecological Indicators, 46, 379–389.
    • (2014) Ecological Indicators , vol.46 , pp. 379-389
    • Yang, C.1    Wang, X.2    Miller, J.A.3    de Blécourt, M.4    Ji, Y.5    Yang, C.6    Harrison, R.D.7    Yu, D.W.8
  • 47
    • 84954390919 scopus 로고    scopus 로고
    • Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
    • 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, 1–14.
    • (2015) Briefings in Bioinformatics , pp. 1-14
    • Zepeda Mendoza, M.L.1    Sicheritz-Ponten, T.2    Gilbert, M.T.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.