Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

ISME Journal

Volumn 6, Issue 3, 2012, Pages 703-707

  Martinez Garcia, Manuel ^a   Brazel, David ^a,b   Poulton, Nicole J ^a   Swan, Brandon K ^a   Gomez, Monica Lluesma ^a   Masland, Dashiell ^a   Sieracki, Michael E ^a   Stepanauskas, Ramunas ^a  

^a BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

^b Health Services and Department of Biology   (United States)

Author keywords

marine; MAST; Pelagibacter; protist; single cell genomics; symbiont

Indexed keywords

SEA WATER;

BACTERIOPLANKTON; BACTERIUM; CELL ORGANELLE; EUKARYOTE; FLOW CYTOMETRY; GENETIC ANALYSIS; GENOMICS; MARINE ECOSYSTEM; MARINE ENVIRONMENT; PREDATOR-PREY INTERACTION; SYMBIOSIS;

ARTICLE; BACTERIUM; CERCOZOA; CHRYSOPHYTA; CLASSIFICATION; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; HETEROTROPHY; MICROBIOLOGY; PHYLOGENY; PILOT STUDY; RNA GENE; SINGLE CELL ANALYSIS;

BACTERIA; CERCOZOA; CHRYSOPHYTA; ECOSYSTEM; GENES, RRNA; HETEROTROPHIC PROCESSES; PHYLOGENY; PILOT PROJECTS; SEAWATER; SINGLE-CELL ANALYSIS; WATER MICROBIOLOGY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CANDIDATUS PELAGIBACTER; CANDIDATUS PELAGIBACTER UBIQUE; CERCOZOA; CHRYSOPHYCEAE; EUKARYOTA; PROKARYOTA; PROTISTA; RICKETTSIALES;

EID: 84857121184     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.126     Document Type: Article

References (32)

1. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741. (Pubitemid 44414595)
2. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-7736. (Pubitemid 41803890)
3. Azam F, Fenchel T, Field JG, Meyer-Reil LA, Thingstad F. (1983). The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10: 257-263.
4. Cheson J. (1983). The estimation and analysis of preference and its relationship to foraging models. Ecology 64: 1297-1304.
5. Ferrantini F, Fokin SI, Modeo L, Andreoli I, Dini F, Görtz HD et al. (2009). ''Candidatus Cryptoprodotis polytropus,'' a novel Rickettsia-like organism in the ciliated protist Pseudomicrothorax dubius (Ciliophora, Nassophorea). J Eukaryot Microbiol 56: 119-129.
6. Fleming EJ, Langdon AE, Martinez-Garcia M, Stepanauskas R, Poulton N, Masland D et al. (2011). What's new is old: Resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH. PLoS ONE 6: E17769.
7. Fu Y, O'Kelly C, Sieracki M, Distal DL. (2003). Protistan grazing analysis by flow cytometry using prey labeled by in vivo expression of fluorescent proteins. Appl Environ Microbiol 69: 6848-6855. (Pubitemid 37420226)
8. Fuhrman JA, McManus GB. (1984). Do bacteria-sized marine eukaryotes consume significant bacterial production? Science 224: 1257-1260.
9. Harada A, Ohtsuka S, Horiguchi T. (2007). Species of the parasitic genus Duboscquella are members of the enigmatic marine Alveolate group I. Protist 158: 337-347. (Pubitemid 47001776)
10. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G et al. (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
11. Heywood JL, Sieracki ME, Bellows W, Poulton NJ, Stepanauskas R. (2011). Capturing diversity of marine heterotrophic protists: One cell at a time. ISME J 5: 674-684.
12. 2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME J 4: 1180-1192.
13. Jasti S, Sieracki ME, Poulton NJ, Giewat MW, Rooney-Varga JN. (2005). Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol 71: 3483-3494. (Pubitemid 40980511)
14. Jezbera J, Horóák K, Šimek K. (2005). Food selection by bacterivorous protists: Insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization. FEMS Microbiol Ecol 52: 351-363. (Pubitemid 40523633)
15. Jezbera J, Hornák K, Simek K. (2006). Prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients. Environ Microbiol 8: 1330-1339. (Pubitemid 44026430)
16. Kneip C, Vobeta C, Lockhart P, Maier U. (2008). The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution. BMC Evol Biol 8: 30.
17. Massana R, Castresana J, Balague V, Guillou L, Romari K, Groisillier A et al. (2004). Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70: 3528-3534. (Pubitemid 38745900)
18. Massana R, Terrado R, Forn I, Lovejoy C, Pedrós-Alió C. (2006). Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environ Microbiol 8: 1515-1522. (Pubitemid 44167978)
19. Massana R, Unrein F, Rodriguez-Martinez R, Forn I, Lefort T, Pinhassi J et al. (2009). Grazing rates and functional diversity of uncultured heterotrophic flagellates. ISME J 3: 588-596.
20. Not F, del Campo J, Balagué V, de Vargas C, Massana R. (2009). New insights into the diversity of marine picoeukaryotes. PLoS ONE 4: E7143.
21. Pernthaler J. (2005). Predation on prokaryotes in the water column and its ecological implications. Nat Rev Micro 3: 537-546. (Pubitemid 40903877)
22. Potvin M, Lovejoy C. (2009). PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries. J Eukaryot Microbiol 56: 174-181.
23. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al. (2007). SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Nucleic Acids Res 35: 7188-7196.
24. Rose JM, Caron DA, Sieracki ME, Poulton N. (2004). Counting heterotrophic nanoplanktonic protists in cultures and aquatic communities by flow cytometry. Aquat Microb Ecol 34: 263-277. (Pubitemid 39098820)
25. Sapp M, Schwaderer A,Wiltshire K, Hoppe H-G, Gerdts G, Wichels A. (2007). Species-specific bacterial communities in the phycosphere of microalgae? Microb Ecol 53: 683-699. (Pubitemid 46763853)
26. Stamatakis A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. (Pubitemid 44642609)
27. Stepanauskas R, Sieracki ME. (2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104: 9052-9057. (Pubitemid 47175435)
28. Worden AZ, Cuvelier ML, Bartlett DH. (2006). In-depth analyses of marine microbial community genomics. Trends Microbiol 14: 331-336. (Pubitemid 44108655)
29. Worden ZA, Not F. (2008). Ecology and diversity of picoeukaryotes. In Kirchman DL (ed), Microbial Ecology of the Oceans. John Wiley & Sons, Inc: Hoboken, New Jersey.
30. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H et al. (2009). Assembling the marine metagenome, one cell at a time. PLoS One 4: E5299.
31. Zhang K, Martiny A, Reppas NB, Barry KW, Malek J, Chrisholm SW et al. (2006). Sequencing genomes from single cells by polymerase cloning. Nat Biotech 24: 680-686. (Pubitemid 43882119)
32. Zubkov MV, Tarran GA. (2008). High bacterivory by the smallest phytoplankton in the North Atlantic Ocean. Nature 455: 224-226.