메뉴 건너뛰기




Volumn 108, Issue , 2014, Pages 17-26

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Author keywords

Benthic patchiness; Deep sea sediment; Environmental DNA; Foraminifera; High throughput sequencing

Indexed keywords

AQUATIC ORGANISMS; DNA; DNA SEQUENCES; POLYMERASE CHAIN REACTION; SEDIMENTS;

EID: 85027924719     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr2.2014.07.018     Document Type: Article
Times cited : (62)

References (66)
  • 1
    • 84986823634 scopus 로고
    • Spatial dispersion of benthic Foraminifera in the abyssal central North Pacific
    • Bernstein B.B., Hessler R.R., Smith R., Jumars P.A. Spatial dispersion of benthic Foraminifera in the abyssal central North Pacific. Limnol. Oceanogr. 1978, 23:401-416.
    • (1978) Limnol. Oceanogr. , vol.23 , pp. 401-416
    • Bernstein, B.B.1    Hessler, R.R.2    Smith, R.3    Jumars, P.A.4
  • 2
    • 0001368668 scopus 로고
    • Temporal persistence of biological patch structure in an abyssal benthic community
    • Bernstein B.B., Meador J.P. Temporal persistence of biological patch structure in an abyssal benthic community. Mar. Biol. 1979, 51:179-183.
    • (1979) Mar. Biol. , vol.51 , pp. 179-183
    • Bernstein, B.B.1    Meador, J.P.2
  • 3
    • 84862007573 scopus 로고    scopus 로고
    • Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill
    • Bik H.M., Halanych K.M., Sharma J., Thomas W.K. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. PLoS One 2012, 7:e38550.
    • (2012) PLoS One , vol.7 , pp. e38550
    • Bik, H.M.1    Halanych, K.M.2    Sharma, J.3    Thomas, W.K.4
  • 6
    • 84867098660 scopus 로고    scopus 로고
    • Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?
    • Carlsen T., Aas A.B., Lindner D., Vrålstad T., Schumacher T., Kauserud H. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?. Fungal Ecol. 2012, 5:747-749.
    • (2012) Fungal Ecol. , vol.5 , pp. 747-749
    • Carlsen, T.1    Aas, A.B.2    Lindner, D.3    Vrålstad, T.4    Schumacher, T.5    Kauserud, H.6
  • 7
    • 84881066986 scopus 로고    scopus 로고
    • Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species
    • Carew M.E., Pettigrove V.J., Metzeling L., Hoffmann A.A. Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Front. Zool. 2013, 10:45.
    • (2013) Front. Zool. , vol.10 , pp. 45
    • Carew, M.E.1    Pettigrove, V.J.2    Metzeling, L.3    Hoffmann, A.A.4
  • 8
    • 66749092157 scopus 로고    scopus 로고
    • A new genus and two new species of saccamminid foraminiferans (Protista, Rhizaria) from the deep Southern Ocean
    • Cedhagen T., Gooday A.J., Pawlowski J. A new genus and two new species of saccamminid foraminiferans (Protista, Rhizaria) from the deep Southern Ocean. Zootaxa 2009, 2096:9-22.
    • (2009) Zootaxa , vol.2096 , pp. 9-22
    • Cedhagen, T.1    Gooday, A.J.2    Pawlowski, J.3
  • 9
    • 78751674645 scopus 로고    scopus 로고
    • Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments
    • Corinaldesi C., Barucca M., Luna G.M., Dell'Anno A. Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Mol. Ecol. 2011, 20:642-654.
    • (2011) Mol. Ecol. , vol.20 , pp. 642-654
    • Corinaldesi, C.1    Barucca, M.2    Luna, G.M.3    Dell'Anno, A.4
  • 10
    • 9644289583 scopus 로고    scopus 로고
    • 'Live' (stained) deep-sea benthic foraminiferans in the western Weddell Sea: trends in abundance, diversity and taxonomic composition along a depth transect
    • Cornelius N., Gooday A.J. 'Live' (stained) deep-sea benthic foraminiferans in the western Weddell Sea: trends in abundance, diversity and taxonomic composition along a depth transect. Deep-Sea Res. II 2004, 51:1571-1602.
    • (2004) Deep-Sea Res. II , vol.51 , pp. 1571-1602
    • Cornelius, N.1    Gooday, A.J.2
  • 12
    • 84879410261 scopus 로고    scopus 로고
    • Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
    • Deagle B.E., Thomas A.C., Shaffer A.K., Trites A.W., Jarman S.N. Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?. Mol. Ecol. Res. 2013, 13:620-633.
    • (2013) Mol. Ecol. Res. , vol.13 , pp. 620-633
    • Deagle, B.E.1    Thomas, A.C.2    Shaffer, A.K.3    Trites, A.W.4    Jarman, S.N.5
  • 13
    • 25844519572 scopus 로고    scopus 로고
    • Extracellular DNA plays a key role in deep-sea ecosystem functioning
    • Dell'Anno A., Danovaro R. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 2005, 309:2179.
    • (2005) Science , vol.309 , pp. 2179
    • Dell'Anno, A.1    Danovaro, R.2
  • 14
    • 33746337635 scopus 로고    scopus 로고
    • A multiple-scale analysis of metazoan meiofaunal distribution in the deep Mediterranean Sea.
    • Gambi C., Danovaro R. A multiple-scale analysis of metazoan meiofaunal distribution in the deep Mediterranean Sea. Deep Sea Res. Part 1 Oceanogr. Res. Pap. 2006, 53:1117-1134.
    • (2006) Deep Sea Res. Part 1 Oceanogr. Res. Pap. , vol.53 , pp. 1117-1134
    • Gambi, C.1    Danovaro, R.2
  • 17
    • 0036822126 scopus 로고    scopus 로고
    • Organic-walled allogromiids: aspects of their occurrence, diversity and ecology in marine habitats
    • Gooday A.J. Organic-walled allogromiids: aspects of their occurrence, diversity and ecology in marine habitats. J. Foraminifer. Res. 2002, 32:384-399.
    • (2002) J. Foraminifer. Res. , vol.32 , pp. 384-399
    • Gooday, A.J.1
  • 18
    • 9644291754 scopus 로고    scopus 로고
    • A new monothalamous foraminiferan from 1000 to 6300m water depth in the Weddell Sea: morphological and molecular characterisation
    • Gooday A.J., Holzmann M., Guiard J., Cornelius N., Pawlowski J. A new monothalamous foraminiferan from 1000 to 6300m water depth in the Weddell Sea: morphological and molecular characterisation. Deep Sea Res. Part II Top. Stud. Oceanogr. 2004, 51:1603-1616.
    • (2004) Deep Sea Res. Part II Top. Stud. Oceanogr. , vol.51 , pp. 1603-1616
    • Gooday, A.J.1    Holzmann, M.2    Guiard, J.3    Cornelius, N.4    Pawlowski, J.5
  • 19
    • 0346422332 scopus 로고    scopus 로고
    • Soft-walled, monothalamous benthic foraminiferans in the Pacific, Indian and Atlantic Oceans: aspects of biodiversity and biogeography
    • Gooday A.J., Hori S., Todo Y., Okamoto T., Kitazato H., Sabbatini A. Soft-walled, monothalamous benthic foraminiferans in the Pacific, Indian and Atlantic Oceans: aspects of biodiversity and biogeography. Deep-Sea Res. 2004, 51:33-53.
    • (2004) Deep-Sea Res. , vol.51 , pp. 33-53
    • Gooday, A.J.1    Hori, S.2    Todo, Y.3    Okamoto, T.4    Kitazato, H.5    Sabbatini, A.6
  • 20
    • 0024487588 scopus 로고
    • Species diversity in deep-sea communities
    • Grassle J.F. Species diversity in deep-sea communities. Trends Ecol. Evol. 1989, 4:12-15.
    • (1989) Trends Ecol. Evol. , vol.4 , pp. 12-15
    • Grassle, J.F.1
  • 21
    • 0026498728 scopus 로고
    • Deep-sea species richness: regional and local diversity estimates from quantitative bottom samples
    • Grassle J.F., Maciolek N.J. Deep-sea species richness: regional and local diversity estimates from quantitative bottom samples. Am. Nat. 1992, 139:313-341.
    • (1992) Am. Nat. , vol.139 , pp. 313-341
    • Grassle, J.F.1    Maciolek, N.J.2
  • 22
    • 0023509634 scopus 로고
    • Macrofaunal colonization of disturbed deep-sea environments and the structure of deep-sea benthic communities
    • Grassle J.F., Morse-Porteous L.S. Macrofaunal colonization of disturbed deep-sea environments and the structure of deep-sea benthic communities. Deep Sea Res. A 1987, 34:1911-1950.
    • (1987) Deep Sea Res. A , vol.34 , pp. 1911-1950
    • Grassle, J.F.1    Morse-Porteous, L.S.2
  • 24
    • 78149397614 scopus 로고    scopus 로고
    • Spatial variability of live benthic foraminiferal faunas on the Portuguese margin
    • Griveaud C., Jorissen F., Anschutz P. Spatial variability of live benthic foraminiferal faunas on the Portuguese margin. Micropaleontology 2010, 297-322.
    • (2010) Micropaleontology , pp. 297-322
    • Griveaud, C.1    Jorissen, F.2    Anschutz, P.3
  • 26
    • 79954587407 scopus 로고    scopus 로고
    • Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
    • Hajibabaei M., Shokralla S., Zhou X., Singer G.A., Baird D.J. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 2011, 6:e17497.
    • (2011) PLoS One , vol.6 , pp. e17497
    • Hajibabaei, M.1    Shokralla, S.2    Zhou, X.3    Singer, G.A.4    Baird, D.J.5
  • 27
    • 49549155295 scopus 로고
    • Abyssal community analysis from replicate box cores in the central North Pacific
    • Hessler R.R., Jumars P.A. Abyssal community analysis from replicate box cores in the central North Pacific. Deep Sea Res. Oceanogr. Abstr. 1974, 21:185-209.
    • (1974) Deep Sea Res. Oceanogr. Abstr. , vol.21 , pp. 185-209
    • Hessler, R.R.1    Jumars, P.A.2
  • 28
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse S.M., Welch D.M., Morrison H.G., Sogin M.L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 2010, 12:1889-1898.
    • (2010) Environ. Microbiol. , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 29
    • 0016958438 scopus 로고
    • Deep-sea species diversity: does it have a characteristic scale?
    • Jumars P.A. Deep-sea species diversity: does it have a characteristic scale?. J. Mar. Res. 1976, 34:217-246.
    • (1976) J. Mar. Res. , vol.34 , pp. 217-246
    • Jumars, P.A.1
  • 30
    • 84898618580 scopus 로고    scopus 로고
    • Using environmental DNA to census marine fishes in a large mesocosm
    • Kelly R.P., Port J.A., Yamahara K.M., Crowder L.B. Using environmental DNA to census marine fishes in a large mesocosm. PloS One 2014, 9:e86175.
    • (2014) PloS One , vol.9 , pp. e86175
    • Kelly, R.P.1    Port, J.A.2    Yamahara, K.M.3    Crowder, L.B.4
  • 31
    • 84884251320 scopus 로고    scopus 로고
    • Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
    • Kozich J.J., Westcott S.L., Baxter N.T., Highlander S.K., Schloss P.D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol 2013.
    • (2013) Appl. Environ. Microbiol
    • Kozich, J.J.1    Westcott, S.L.2    Baxter, N.T.3    Highlander, S.K.4    Schloss, P.D.5
  • 33
    • 66749166464 scopus 로고    scopus 로고
    • Global genetic homogeneity in deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae)
    • Lecroq B., Gooday A.J., Pawlowski J. Global genetic homogeneity in deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae). Zootaxa 2009, 2096:23-32.
    • (2009) Zootaxa , vol.2096 , pp. 23-32
    • Lecroq, B.1    Gooday, A.J.2    Pawlowski, J.3
  • 35
    • 84866065801 scopus 로고    scopus 로고
    • Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing
    • Lee C.K., Herbold C.W., Polson S.W., Wommack K.E., Williamson S.J., McDonald I.R., Cary S.C. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 2012, 7:e44224.
    • (2012) PLoS One , vol.7 , pp. e44224
    • Lee, C.K.1    Herbold, C.W.2    Polson, S.W.3    Wommack, K.E.4    Williamson, S.J.5    McDonald, I.R.6    Cary, S.C.7
  • 37
    • 84874325671 scopus 로고    scopus 로고
    • Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach
    • Lejzerowicz F., Voltsky I., Pawlowski J. Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach. Deep-Sea Res. II 2013, 86:214-220.
    • (2013) Deep-Sea Res. II , vol.86 , pp. 214-220
    • Lejzerowicz, F.1    Voltsky, I.2    Pawlowski, J.3
  • 38
  • 39
    • 0002996125 scopus 로고
    • Effects of giant protozoans (class: Xenophyophorea) on deep-seamount benthos
    • Levin L.A., DeMaster D.J., McCann L.D., Thomas C.L. Effects of giant protozoans (class: Xenophyophorea) on deep-seamount benthos. Mar. Ecol. Prog. Ser. 1986, 29:99-104.
    • (1986) Mar. Ecol. Prog. Ser. , vol.29 , pp. 99-104
    • Levin, L.A.1    DeMaster, D.J.2    McCann, L.D.3    Thomas, C.L.4
  • 41
    • 84873940355 scopus 로고    scopus 로고
    • Selective settlement of deep-sea canyon nematodes after resuspension-an experimental approach
    • Lins L., Vanreusel A., van Campenhout J., Ingels J. Selective settlement of deep-sea canyon nematodes after resuspension-an experimental approach. J. Exp. Mar. Biol. Ecol. 2013, 441:110-116.
    • (2013) J. Exp. Mar. Biol. Ecol. , vol.441 , pp. 110-116
    • Lins, L.1    Vanreusel, A.2    van Campenhout, J.3    Ingels, J.4
  • 44
    • 84859408606 scopus 로고    scopus 로고
    • Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves
    • McClain C.R., Stegen J.C., Hurlbert A.H. Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves. Proc. R. Soc. B: Biol. Sci. 2012, 279:1993-2002.
    • (2012) Proc. R. Soc. B: Biol. Sci. , vol.279 , pp. 1993-2002
    • McClain, C.R.1    Stegen, J.C.2    Hurlbert, A.H.3
  • 45
    • 79961162493 scopus 로고    scopus 로고
    • Deep-sea nematode assemblage has not recovered 26 years after experimental mining of polymetallic nodules (Clarion-Clipperton Fracture Zone, Tropical Eastern Pacific)
    • Miljutin D.M., Miljutina M.A., Arbizu P.M., Galéron J. Deep-sea nematode assemblage has not recovered 26 years after experimental mining of polymetallic nodules (Clarion-Clipperton Fracture Zone, Tropical Eastern Pacific). Deep-Sea Res. I 2011, 58:885-897.
    • (2011) Deep-Sea Res. I , vol.58 , pp. 885-897
    • Miljutin, D.M.1    Miljutina, M.A.2    Arbizu, P.M.3    Galéron, J.4
  • 46
    • 84891719992 scopus 로고    scopus 로고
    • How much metagenomic sequencing is enough to achieve a given goal?
    • Ni J., Yan Q., Yu Y. How much metagenomic sequencing is enough to achieve a given goal?. Sci. Rep. 2013, 3:1968.
    • (2013) Sci. Rep. , vol.3 , pp. 1968
    • Ni, J.1    Yan, Q.2    Yu, Y.3
  • 48
    • 84873906604 scopus 로고    scopus 로고
    • Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces
    • Orsi W., Biddle J.F., Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PloS One 2013, 8:e56335.
    • (2013) PloS One , vol.8 , pp. e56335
    • Orsi, W.1    Biddle, J.F.2    Edgcomb, V.3
  • 52
    • 84894337606 scopus 로고    scopus 로고
    • A plea for DNA barcoding of Foraminifera
    • Pawlowski J., Holzmann M. A plea for DNA barcoding of Foraminifera. J. Foraminifer. Res. 2014, 44:62-67.
    • (2014) J. Foraminifer. Res. , vol.44 , pp. 62-67
    • Pawlowski, J.1    Holzmann, M.2
  • 54
    • 84877880477 scopus 로고    scopus 로고
    • New supraordinal classification of Foraminifera: molecules meet morphology
    • Pawlowski J., Holzmann M., Tyszka J. New supraordinal classification of Foraminifera: molecules meet morphology. Mar. Micropaleontol. 2013, 100:1-10.
    • (2013) Mar. Micropaleontol. , vol.100 , pp. 1-10
    • Pawlowski, J.1    Holzmann, M.2    Tyszka, J.3
  • 55
    • 77952625912 scopus 로고    scopus 로고
    • Short rDNA barcodes for species identification in foraminifera
    • Pawlowski J., Lecroq B. Short rDNA barcodes for species identification in foraminifera. J. Eukaryot. Microbiol. 2010, 57:197-205.
    • (2010) J. Eukaryot. Microbiol. , vol.57 , pp. 197-205
    • Pawlowski, J.1    Lecroq, B.2
  • 56
    • 84907953277 scopus 로고    scopus 로고
    • Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities.
    • (in press).
    • Pawlowski, J., Esling, P., Lejzerowicz, F., Cedhagen, T., Wilding, T.A. 2014. Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities. Mol. Ecol. Resour. (in press). http://dx.doi.org/10.1111/1755-0998.12261.
    • (2014) Mol. Ecol. Resour.
    • Pawlowski, J.1    Esling, P.2    Lejzerowicz, F.3    Cedhagen, T.4    Wilding, T.A.5
  • 57
    • 0028586213 scopus 로고
    • Patch dynamics in the deep-sea benthos: the role of a heterogeneous supply of organic matter
    • Blackwell Scientific Publications, Oxford, P.S. Guller, A.G. Hildrew, D.G. Raffaelli (Eds.)
    • Rice A.L., Lambshead P.J.D. Patch dynamics in the deep-sea benthos: the role of a heterogeneous supply of organic matter. Aquatic Ecology: Scale Pattern and Process 1994, 469-498. Blackwell Scientific Publications, Oxford. P.S. Guller, A.G. Hildrew, D.G. Raffaelli (Eds.).
    • (1994) Aquatic Ecology: Scale Pattern and Process , pp. 469-498
    • Rice, A.L.1    Lambshead, P.J.D.2
  • 60
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS one 2011, 6:e27310.
    • (2011) PloS one , vol.6 , pp. e27310
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 63
    • 0141541981 scopus 로고    scopus 로고
    • A riot of species in an environmental calm: the paradox of the species-rich deepsea floor
    • Snelgrove P.V.R., Smith C.R. A riot of species in an environmental calm: the paradox of the species-rich deepsea floor. Oceanogr. Mar. Biol.: Annu. Rev. 2002, 40:311-342.
    • (2002) Oceanogr. Mar. Biol.: Annu. Rev. , vol.40 , pp. 311-342
    • Snelgrove, P.V.R.1    Smith, C.R.2
  • 64
    • 84874197057 scopus 로고    scopus 로고
    • Can abundance of protists be inferred from sequence data: a case study of foraminifera
    • Weber A.A., Pawlowski J. Can abundance of protists be inferred from sequence data: a case study of foraminifera. PloS One 2013, 8:e56739.
    • (2013) PloS One , vol.8 , pp. e56739
    • Weber, A.A.1    Pawlowski, J.2
  • 66
    • 13844317082 scopus 로고    scopus 로고
    • Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene
    • Zhu F., Massana R., Not F., Marie D., Vaulot D. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 2005, 52:79-92.
    • (2005) FEMS Microbiol. Ecol. , vol.52 , pp. 79-92
    • Zhu, F.1    Massana, R.2    Not, F.3    Marie, D.4    Vaulot, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.