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Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.

Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP.

BMC Biol. 2009 Nov 3;7:72. doi: 10.1186/1741-7007-7-72.


Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water.

Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA.

Mol Ecol. 2010 Mar;19 Suppl 1:21-31. doi: 10.1111/j.1365-294X.2009.04480.x.


Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness.

Edgcomb V, Orsi W, Bunge J, Jeon S, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R, Epstein S.

ISME J. 2011 Aug;5(8):1344-56. doi: 10.1038/ismej.2011.6. Epub 2011 Mar 10.


Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.

Lie AA, Liu Z, Hu SK, Jones AC, Kim DY, Countway PD, Amaral-Zettler LA, Cary SC, Sherr EB, Sherr BF, Gast RJ, Caron DA.

Appl Environ Microbiol. 2014 Jul;80(14):4363-73. doi: 10.1128/AEM.00057-14. Epub 2014 May 9.


The dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing.

Rodriguez-Mora MJ, Scranton MI, Taylor GT, Chistoserdov AY.

FEMS Microbiol Ecol. 2015 Sep;91(9):fiv088. doi: 10.1093/femsec/fiv088. Epub 2015 Jul 23.


Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column.

Jeon SO, Bunge J, Stoeck T, Barger KJ, Hong SH, Epstein SS.

Appl Environ Microbiol. 2006 Oct;72(10):6578-83.


Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity.

Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D.

PLoS One. 2013;8(3):e58950. doi: 10.1371/journal.pone.0058950. Epub 2013 Mar 14.


Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML.

PLoS Genet. 2008 Nov;4(11):e1000255. doi: 10.1371/journal.pgen.1000255. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851. Welch, David Mark [corrected to Mark Welch, David].


Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study.

Bachy C, Dolan JR, López-García P, Deschamps P, Moreira D.

ISME J. 2013 Feb;7(2):244-55. doi: 10.1038/ismej.2012.106. Epub 2012 Oct 4.


Rapid shifts in the structure and composition of a protistan assemblage during bottle incubations affect estimates of total protistan species richness.

Kim DY, Countway PD, Gast RJ, Caron DA.

Microb Ecol. 2011 Aug;62(2):383-98. doi: 10.1007/s00248-011-9816-9. Epub 2011 Mar 4.


Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway).

Behnke A, Bunge J, Barger K, Breiner HW, Alla V, Stoeck T.

Appl Environ Microbiol. 2006 May;72(5):3626-36.


A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples.

Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS.

Protist. 2006 Feb;157(1):31-43. Epub 2006 Jan 23.


New insights into the diversity of marine picoeukaryotes.

Not F, del Campo J, Balagué V, de Vargas C, Massana R.

PLoS One. 2009 Sep 29;4(9):e7143. doi: 10.1371/journal.pone.0007143.


Effect of oxygen minimum zone formation on communities of marine protists.

Orsi W, Song YC, Hallam S, Edgcomb V.

ISME J. 2012 Aug;6(8):1586-601. doi: 10.1038/ismej.2012.7. Epub 2012 Mar 8.


Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin.

Alexander E, Stock A, Breiner HW, Behnke A, Bunge J, Yakimov MM, Stoeck T.

Environ Microbiol. 2009 Feb;11(2):360-81. doi: 10.1111/j.1462-2920.2008.01777.x. Epub 2008 Sep 26.


Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream).

Countway PD, Gast RJ, Dennett MR, Savai P, Rose JM, Caron DA.

Environ Microbiol. 2007 May;9(5):1219-32.


Eukaryotic richness in the abyss: insights from pyrotag sequencing.

Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L.

PLoS One. 2011 Apr 4;6(4):e18169. doi: 10.1371/journal.pone.0018169.


Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization.

Orsi W, Edgcomb V, Jeon S, Leslin C, Bunge J, Taylor GT, Varela R, Epstein S.

ISME J. 2011 Aug;5(8):1357-73. doi: 10.1038/ismej.2011.7. Epub 2011 Mar 10.


A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.

Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM.

PLoS One. 2009 Jul 27;4(7):e6372. doi: 10.1371/journal.pone.0006372. Erratum in: PLoS One. 2009;4(12). doi: 10.1371/annotation/50c43133-0df5-4b8b-8975-8cc37d4f2f26.


Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods.

Santoferrara LF, Grattepanche JD, Katz LA, McManus GB.

Environ Microbiol. 2014 Sep;16(9):2752-63. doi: 10.1111/1462-2920.12380. Epub 2014 Feb 18.


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