Danovaro R. Extending the approaches of biodiversity and ecosystem functioning to the deep ocean. In: Solan M, Aspden RJ, Paterson DM, editors. Marine biodiversity and ecosystem functioning: frameworks, methodologies, and integration. Oxford: Oxford University Press; 2012. p. 115–26.
Chapter
Google Scholar
Creer S, Sinniger F. Cosmopolitanism of microbial eukaryotes in the global deep seas. Mol Ecol. 2012;21:1033–5.
Article
PubMed
Google Scholar
Pitcher TJ, Morato T, Hart PJB, Clark MR, Haggan N, Santos RS. Seamounts: ecology, fisheries, and conservation. Oxford: Blackwell; 2007.
Book
Google Scholar
Clark MR, Rowden AA, Schlacher T, Williams A, Consalvey M, Stocks KI, Rogers AD, O’Hara TD, White M, Shank TM, Hall-Spencer JM. The ecology of seamounts: structure, function, and human impacts. Annu Rev Mar Sci. 2010;2:253–78.
Article
Google Scholar
Ramirez-Llodra E, Brandt A, Danovaro R, De Mol B, Escobar E, German CR, Levin LA, Martinez Arbizu P, Menot L, Buhl-Mortensen P, Narayanaswamy BE, Smith CR, Tittensor DP, Tyler PA, Vanreusel A, Vecchione M. Deep, diverse and definitely different: unique attributes of the world’s largest ecosystem. Biogeosciences. 2010;7:2851–99.
Article
Google Scholar
Stefanoudis PV, Bett BJ, Gooday AJ. Abyssal hills: influence of topography on benthic foraminiferal assemblages. Prog Oceanogr. 2016;148:44–55.
Article
Google Scholar
Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L. Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One. 2011;6:4.
Google Scholar
Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol Ecol. 2012;21:1048–59.
Article
PubMed
Google Scholar
Edgcomb VP, Kysela DT, Teske A, Gomez AD, Sogin ML. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci U S A. 2002;99:7658–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
López-García P, Philippe H, Gail F, Moreira D. Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the mid-Atlantic ridge. Proc Natl Acad Sci U S A. 2003;100:697–702.
Article
PubMed
PubMed Central
Google Scholar
López-García P, Vereshchaka A, Moreira D. Eukaryotic diversity associated with carbonates and fluid-seawater interface in lost City hydrothermal field. Environ Microbiol. 2007;9:546–54.
Article
PubMed
Google Scholar
Sauvadet AL, Gobet A, Guillou L. Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats. Environ Microbiol. 2010;12:2946–64.
Article
CAS
PubMed
Google Scholar
Urich T, Lanzen A, Stokke R, Pedersen RB, Bayer C, Thorseth IH, Schleper C, Steen IH, Ovreas L. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ Microbiol. 2014;16:2699–710.
Article
CAS
PubMed
Google Scholar
Hausmann K, Hulsmann N, Polianski I, Schade S, Weitere M. Composition of benthic protozoan communities along a depth transect in the eastern Mediterranean Sea. Deep-Sea Res I. 2002;49:1959–70.
Article
Google Scholar
Pachiadaki MG, Taylor C, Oikonomou A, Yakimov MM, Stoeck T, Edgcomb V. In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs. Deep Sea Res II. 2016;129:223–31.
Article
Google Scholar
Gong J, Shi F, Ma B, Dong J, Pachiadaki M, Zhang X, Edgcomb VP. Depth shapes alpha- and beta-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems. Environ Microbiol. 2015;17:3722–37.
Article
CAS
PubMed
Google Scholar
Fenchel T. The ecology of marine microbenthos. IV structure and function of the benthic ecosystem, its chemical and physical factors and the microfauna communities with special reference to the ciliated protozoa. Ophelia. 1969;6:1–182.
Article
Google Scholar
Berninger UG, Epstein SS. Vertical distribution of benthic ciliates in response to the oxygen concentration in an intertidal North Sea sediment. Aquat Microb Ecol. 1995;9:229–36.
Article
Google Scholar
Carey PC. Marine interstitial ciliates: an illustrated key. New York: Chapman and Hall; 1992.
Google Scholar
Hamels I, Muylaert K, Sabbe K, Vyverman W. Contrasting dynamics of ciliate communities in sandy and silty sediments of an estuarine intertidal flat. Eur J Protistol. 2005;41:241–50.
Article
Google Scholar
Zhao F, Xu K. Distribution of ciliates in intertidal sediments across geographic distances: a molecular view. Protist. 2017;168:172–81.
Article
Google Scholar
Zhao F, Xu K. Molecular diversity and distribution pattern of ciliates in sediments from deep-sea hydrothermal vents in the Okinawa trough and adjacent sea areas. Deep-Sea Res I. 2016;116:22–32.
Article
Google Scholar
Forster D, Dunthorn M, Mahe F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra W, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T. Benthic protists: the under-charted majority. FEMS Microbiol Ecol. 2016;92:8.
Article
Google Scholar
Meng Z, Xu K, Dai R, Lei Y. Ciliate community structure, diversity and trophic role in offshore sediments from the Yellow Sea. Eur J Protistol. 2012;48:73–84.
Article
PubMed
Google Scholar
Scheckenbach F, Hausmann K, Wylezich C, Weitere M, Arndt H. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. Proc Natl Acad Sci U S A. 2010;107:115–20.
Article
CAS
PubMed
Google Scholar
Lejzerowicz F, Esling P, Pawlowski J. Patchiness of deep-sea benthic foraminifera across the Southern Ocean: insights from high-throughput DNA sequencing. Deep-Sea Res II. 2014;108:17–26.
Article
CAS
Google Scholar
Coyne KJ, Countway PD, Pilditch CA, Lee CK, Caron DA, Cary SC. Diversity and distributional patterns of ciliates in Guaymas Basin hydrothermal vent sediments. J Eukaryot Microbiol. 2013;60:433–47.
Article
CAS
PubMed
Google Scholar
Takishita K, Kakizoe N, Yoshida T, Maruyama T. Molecular evidence that phylogenetically diverged ciliates are active in microbial mats of deep-sea cold-seep sediment. J Eukaryot Microbiol. 2010;57:76–86.
Article
CAS
PubMed
Google Scholar
Du Y, Xu K, Warren A, Lei Y, Dai R. Benthic ciliate and meiofaunal communities in two contrasting habitats of an intertidal estuarine wetland. J Sea Res. 2012;70:50–63.
Article
Google Scholar
Fu R, Gong J. Single cell analysis linking ribosomal (r)DNA and rRNA copy numbers to cell size and growth rate provides insights into molecular protistan ecology. J Eukaryot Microbiol. 2017; 10.1111/jeu.12425.
Esteban G, Finlay BJ, Embley TM. New species double the diversity of anaerobic ciliates in a Spanish lake. FEMS Microbiol Lett. 1993;109:93–100.
Article
Google Scholar
Wang Y, Song W, Warren A, Al-Rasheid KAS, Al-Quraishy SA, Al-Farraj SA, Hu X, Pan H. Descriptions of two new marine scuticociliates, Pleuronema sinica n. Sp and P. wilberti n. Sp (Ciliophora: Scuticociliatida), from the Yellow Sea, China. Eur J Protistol. 2009;45:29–37.
Article
CAS
PubMed
Google Scholar
Caron DA, Countway PD. Hypotheses on the role of the protistan rare biosphere in a changing world. Aquat Microb Ecol. 2009;57:227–38.
Article
Google Scholar
Pedrós-Alió C. The rare bacterial biosphere. Annu Rev Mar Sci. 2012;4:449–66.
Article
Google Scholar
Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D'Hondt S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci U S A. 2012;109:16213–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parkes RJ, Cragg BA, Wellsbury P. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J. 2000;8:11–28.
Article
Google Scholar
Coolen MJL, Saenz JP, Giosan L, Trowbridge NY, Dimitrov P, Dimitrov D, Eglinton TI. DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene. Earth Planet Sci Lett. 2009;284:610–21.
Article
CAS
Google Scholar
Stoeck T, Zuendorf A, Breiner HW, Behnke A. A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microb Ecol. 2007;53:328–39.
Article
CAS
PubMed
Google Scholar
Jones SE, Lennon JT. Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci U S A. 2010;107:5881–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, Richards TA. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.
Article
CAS
PubMed
Google Scholar
Gong J, Dong J, Liu XH, Massana R. Extremely high copy numbers and polymorphisms of the rDNA operon estimated from single cell analysis of Oligotrich and Peritrich ciliates. Protist. 2013;164:369–79.
Article
CAS
PubMed
Google Scholar
Weber AAT, Pawlowski J. Wide occurrence of SSU rDNA intragenomic polymorphism in foraminifera and its implications for molecular species identification. Protist. 2014;165:645–61.
Article
CAS
PubMed
Google Scholar
Balzano S, Abs E, Leterme SC. Protist diversity along a salinity gradient in a coastal lagoon. Aquat Microb Ecol. 2015;74:263–77.
Article
Google Scholar
Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra W, Logares R, Mahe F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environ Microbiol. 2015;17:4035–49.
Article
CAS
PubMed
Google Scholar
Nebel M, Pfabel C, Stock A, Dunthorn M, Stoeck T. Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environ Microbiol Reports. 2011;3:154–8.
Article
CAS
Google Scholar
Dunthorn M, Klier J, Bunge J, Stoeck T. Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity. J Eukaryot Microbiol. 2012;59:185–7.
Article
CAS
PubMed
Google Scholar
Filker S, Gimmler A, Dunthorn M, Mahe F, Stoeck T. Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds. Extremophiles. 2015;19:283–95.
Article
CAS
PubMed
Google Scholar
Orsi W, Edgcomb V, Faria J, Foissner W, Fowle WH, Hohmann T, Suarez P, Taylor C, Taylor GT, Vd'acny P, Epstein SS. Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin. Venezuela Int J Syst Evol Microbiol. 2012;62:1425–33.
Article
CAS
PubMed
Google Scholar
Gimmler A, Stoeck T. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. Environ Microbiol Reports. 2015;7:679–86.
Article
CAS
Google Scholar
Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol. 2013;13:150.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Article
CAS
PubMed
Google Scholar
Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459:193–9.
Article
CAS
PubMed
Google Scholar
Jost L. Partitioning diversity into independent alpha and beta components. Ecology. 2007;88:2427–39.
Article
PubMed
Google Scholar
Hennig C. Cluster-wise assessment of cluster stability. Comput Stat Data An. 2007;52:258–71.
Article
Google Scholar
Hennig C. Dissolution point and isolation robustness: robustness criteria for general cluster analysis methods. J Multivar Anal. 2008;99:1154–76.
Article
Google Scholar
Oksanen J, Guillaume BF, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. Vegan: community ecology package. R package version 1.17-3. 2010. http://CRAN.R-project.org/package=vegan
Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci. 1996;12:543.
CAS
PubMed
Google Scholar
Csárdi G, Nepusz T. The igraph software package for complex network research. Inter J Complex Syst. 2006;1695:1–9.
Google Scholar
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. ICWSM. 2009;8:361–2.
Google Scholar