Abstract
Environmental factors restrict the distribution of microbial eukaryotes but the exact boundaries for eukaryotic life are not known. Here, we examine protistan communities at the extremes of salinity and osmotic pressure, and report rich assemblages inhabiting Bannock and Discovery, two deep-sea superhaline anoxic basins in the Mediterranean. Using a rRNA-based approach, we detected 1,538 protistan rRNA gene sequences from water samples with total salinity ranging from 39 to 280 g/Kg, and obtained evidence that this DNA was endogenous to the extreme habitat sampled. Statistical analyses indicate that the discovered phylotypes represent only a fraction of species actually inhabiting both the brine and the brine-seawater interface, with as much as 82% of the actual richness missed by our survey. Jaccard indices (e.g., for a comparison of community membership) suggest that the brine/interface protistan communities are unique to Bannock and Discovery basins, and share little (0.8–2.8%) in species composition with overlying waters with typical marine salinity and oxygen tension. The protistan communities from the basins’ brine and brine/seawater interface appear to be particularly enriched with dinoflagellates, ciliates and other alveolates, as well as fungi, and are conspicuously poor in stramenopiles. The uniqueness and diversity of brine and brine-interface protistan communities make them promising targets for protistan discovery.
Similar content being viewed by others
Abbreviations
- DHAB:
-
Deep hypersaline anoxic basin
- UMA:
-
Uncultured marine alveolate clade
References
Azam F, Fenchel T, Field J, Gray J, Meyer-Reil L, Thingstad F (1983) The ecological role of water column microbes in the sea. Mar Ecol Prog Ser 10:257–263
Beaver JR, Crisman TL (1982) The trophic response of ciliated protozoans in freshwater lakes. Limnol Oceanogr 27:246–253
Behnke A, Bunge J, Barger K, Breiner HW, Alla V, Stoeck T (2006) Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic Fjord (Framvaren, Norway). Appl Environ Microbiol 72:3626–3636
Camerlenghi A (1990) Anoxic basins of the eastern Mediterranean: geological framework. Mar Chem 31:1–19
Chao A, Shen TJ (2003–2005) http://chao.stat.nthu.edu.tw
Chao A, Chazdon RL, Colwell RK, Shen TJ (2006) Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62:361–371
Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA et al (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443
Coleman RG (1993) Geological evolution of the Red Sea, vol 24. Clarendon Press, Oxford, p 138
Countway PD, Gast RJ, Dennett MR, Savai P, Rose JM, Caron DA (2007) Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Environ Microbiol 9:1219–1232
Daffonchio D, Borin S, Brusa T, Brusetti L, van der Wielen PW, Bolhuis H et al (2006) Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline. Nature 440:203–207
Danovaro R, Corinaldesi C, Dell’Anno A, Fabiano M, Corselli C (2005) Viruses, prokaryotes and DNA in the sediments of a deep-hypersaline anoxic basin (DHAB) of the Mediterranean Sea. Environ Microbiol 7:586–592
Dawson SC, Pace NR (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99:8324–8329
de Lange GJ, Middelburg JJ, van der Weijden CH, Catalano G, Luther IGW, Hydes DJ et al (1990) Composition of anoxic hypersaline brines in the Tyro and Bannock Basins, eastern Mediterranean. Mar Chem 31:63–88
Dighton J (2003) Fungi in ecosystem processes, vol. 17, 1st edn. Marcel Dekker Inc, New York
Dumitru R, Hornby JM, Nickerson KW (2004) Defined anaerobic growth medium for studying Candida albicans basic biology and resistance to eight antifungal drugs. Antimicrob Agents Chemother 48:2350–2354
Eder W, Ludwig W, Huber R (1999) Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of kebrit deep, red Sea. Arch Microbiol 172:213–218
Eder W, Jahnke LL, Schmidt M, Huber R (2001) Microbial diversity of the brine-seawater interface of the Kebrit Deep, Red Sea, studied via 16S rRNA gene sequences and cultivation methods. Appl Environ Microbiol 67:3077–3085
Eder W, Schmidt M, Koch M, Garbe-Schonberg D, Huber R (2002) Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea. Environ Microbiol 4:758–763
Edgcomb VP, Kysela DT, Teske A, de Vera Gomez A, Sogin ML (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci USA 99:7658–7662
Ehrenberg CC (1838) Die Infusionstierchen als vollkommene Organismen. Ein Blick in das tiefere organische Leben der Natur. Voss: Leipzig, Germany, 547 pp
Elloumi J, Carrias J-F, Ayadi H, Sime-Ngando T, Boukhris M, Bouaïn A (2006) Composition and distribution of planktonic ciliates from ponds of different salinity in the solar saltwork of Sfax, Tunisia. Estuar Coast Shelf Sci 67:21–29
Epstein SS (1995) Simultaneous enumeration of protozoa and micrometazoa from marine sandy sediments. Aquat Microb Ecol 9:219–227
Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185
Fell JW, Boekhout T, Fonseca A, Sampaio JP (2001) Basidiomycetous yeast. In: McLaughlin EG, Lemke PA (eds) The mycota: systemics and evolution, 1st edn. Springer, Berlin
Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, dos Santos VAPM, Yakimov MM et al (2005) Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12:895–904
Finlay BJ (1990) Physiological ecology of free-living protozoa. Adv Microbiol Ecol 11:1–34
Foissner W (2008) Diversity and distribution of ciliates (Protista: Ciliophora). Biodivers Conserv 17:345–363
Gates MA, Rogerson A, Berger J (1982) Dry to wet weight biomass conversion constant for Tetrahymena elliott. Oecologia 55:145–148
Gunde-Cimerman N, Zalar P, de Hoog S, Plemenitasd A (2000) Hypersaline waters in salterns—natural ecological niches for halophilic black yeasts. FEMS Microbiol Ecol 32:235–240
Gunde-Cimerman N, Oren A, Plemenitasd A (2005). Adaptation to life at high salt concentrations in archaea, bacteria and eukarya. Springer, Dordrecht, p 577
Hallsworth JE, Yakimov MM, Golyshin PN, Gillion JL, D’Auria G, Lima Alves F et al (2007) Limits of life in MgCl2-containing environments: chaotropicity defines the window. Environ Microbiol 9:801–813
Hauer G, Rogerson A (2005) Heterotrophic protozoa from hypersaline environments. In: Gunde-Cimerman N, Oren A, Plemenitasd A (eds) Adaptation to life at high salt concentrations in archaea, bacteria, and eukarya. Springer, Dordrecht, pp 519–540
Hong SH, Bunge J, Jeon SO, Epstein SS (2006) Predicting microbial species richness. Proc Natl Acad Sci USA 103:117–122
Horowitz NH, Cameron RE, Hubbard JS (1972) Microbiology of the dry valleys of Antarctica. Science 176:242–245
Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
Javor B (1989) Hypersaline environments, microbiology and biogeochemistry. Springer, Berlin
Jeon SO, Bunge J, Stoeck T, Barger K, Hong S-H, Epstein S (2006) Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column. Appl Environ Microbiol 72:6578–6583
Kahl DM (1930–1935) Urtiere oder Protozoa I. Gustav Fischer: Jena, Germany
Kis-Papo T, Grishkan I, Oren A, Wasser SP, Nevo E (2001) Spatiotemporal diversity of filamentous fungi in the hypersaline Dead Sea. Mycol Res 105:749–756
López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603–607
López-García P, Philippe H, Gail F, Moreira D (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc Natl Acad Sci USA 100:697–702
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371
Luo Q, Krumholz LR, Najar FZ, Peacock AD, Roe BA, White DC et al (2005) Diversity of the microeukaryotic community in sulfide-rich Zodletone Spring (Oklahoma). Appl Environ Microbiol 71:6175–6184
Mansfield SD, Barlocher F (1993) Seasonal variation of fungal biomass in the sediment of a salt marsh in New Brunswick. Microb Ecol 26:37–45
Massana R, Guillou L, Díez B, Pedrós-Alió C (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol 68:4554–4558
Massana R, Balagué V, Guillou L, Pedrós-Alió C (2004a) Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 50:231–243
Massana R, Castresana J, Balagué V, Guillou L, Romari K, Groisillier A et al (2004b) Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70:3528–3534
Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491–499
Moon-van der Staay SY, De Wachter R, Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607–610
Nagahama T, Hamamoto M, Nakase T, Takaki Y, Horikoshi K (2003) Cryptococcus surugaensis sp. nov., a novel yeast species from sediment collected on the deep-sea floor of Suruga Bay. Int J Syst Evol Microbiol 53:2095–2098
Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ (2007) Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ Microbiol 9:1233–1252
Oren A (1999) Microbiological studies in the Dead Sea: future challenges toward the understanding of life at the limit of salt concentrations. Hydrobiologia 405:1–9
Oren A (2000) Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. J Ind Microbiol Biotechnol 28:56–63
Oren A (2002) Halophilic microorganisms and their environments. Kluwer Academic Publishers, Dordrecht, p 575
Pedrós-Alió C, Calderón-Paz JI, MacLean MH, Medina G, Marrasé C, Gasol JM et al (2000) The microbial food web along salinity gradients. FEMS Microbiol Ecol 32:143–155
Por F (1980) A classification of hypersaline waters, based on trophic criteria. Mar Ecol 1:121–131
Posada D, Crandall KA (2001) Selecting the best-fit model of nucleotide substitution. Syst Biol 50:580–601
Ramos-Cormenzana A (1991) Halophilic organisms and their environment. In: Rodríguez-Valera F (ed) General and applied aspects of halophilic microorganisms. Plenum Press, New York, pp 15–24
Romari K, Vaulot D (2004) Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol Oceanogr 49:784–798
Sass AM, Sass H, Coolen MJ, Cypionka H, Overmann J (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea). Appl Environ Microbiol 67:5392–5402
Siegel BZ, McMurty G, Siegel SM, Chen J, Larock P (1979) Life in the calcium-chloride environment of Don-Juan Pond, Antarctica. Nature 280:828–829
Sonderegger M, Jeppsson M, Hahn-Hagerdal B, Sauer U (2004) Molecular basis for anaerobic growth of Saccharomyces cerevisiae on xylose, investigated by global gene expression and metabolic flux analysis. Appl Environ Microbiol 70:2307–2317
Stoeck T, Epstein S (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69:2657–2663
Stoeck T, Fowle WH, Epstein SS (2003a) Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images. Appl Environ Microbiol 69:6856–6863
Stoeck T, Taylor GT, Epstein SS (2003b) Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl Environ Microbiol 69:5656–5663
Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157:31–43
Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S (2007) Protistan diversity in the arctic: a case of paleoclimate shaping modern biodiversity? PLoS ONE 2:e728
Stoecker DK (1999) Mixotrophy among dinoflagellates. J Euk Microbiol 46:397–401
Swofford DL (2002) Sinauer Associates Inc., Sunderland, MA
Takishita K, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T (2007) Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles 11:563–576
Taylor GT, Scranton MI, Iabichella I, Ho T-Y, Thunell RC, Muller-Karger F et al (2001) Chemoautotrophy in the redox transition zone of the Cariaco Basin: a significant midwater source of organic carbon production. Limnol Oceanogr 46:148–163
Taylor GT, Labichella-Armas M, Varela R, Müller-Karger F, Lin X, Scranton MI (2006) Microbial ecology of the Cariaco basin’s redoxcline. In: Neretin NL (ed) Past and present water column anoxia. Springer, Dordrecht, pp 473–499
van der Wielen PW, Heijs SK (2007) Sulfate-reducing prokaryotic communities in two deep hypersaline anoxic basins in the Eastern Mediterranean deep sea. Environ Microbiol 9:1335–1340
van der Wielen PW, Bolhuis H, Borin S, Daffonchio D, Corselli C, Giuliano L et al (2005) The enigma of prokaryotic life in deep hypersaline anoxic basins. Science 307:121–123
Wallmann KJ, Suess E, Westbrook GH, Winckler G, Cita MB (1997) Salty brines on the Mediterranean sea floor. Nature 387:31–32
Wallmann K, Aghib FS, Castradori D, Cita MB, Suess E, Greinert J et al (2002) Sedimentation and formation of secondary minerals in the hypersaline Discovery Basin, eastern Mediterranean. Mar Geol 186:9–28
Worden AZ (2006) Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquat Microb Ecol 43:165–175
Wright AD, Colorni A (2002) Taxonomic re-assignment of Cryptocaryon irritans, a marine fish parasite. Europ J Protistol 37:375–378
Yakimov MM, Giuliano L, Cappello S, Denaro R, Golyshin PN (2007a) Microbial community of a hydrothermal mud vent underneath the deep-sea anoxic brine lake Urania (eastern Mediterranean). Orig Life Evol Biosph 37:177–188
Yakimov MM, La Cono V, Denaro R, D’Auria G, Decembrini F, Timmis KN et al (2007b) Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L’Atalante, Eastern Mediterranean Sea. ISME J 1:743–755
Zubkov MV, Burkhill PH, Topping J (2007) Flow cytometric enumeration of DNA-stained oceanic planktonic protists. J Plankt Res 29:79–86
Zuendorf A, Behnke A, Bunge J, Barger K, Stoeck T (2006) Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol Ecol 58:476–491
Acknowledgments
This study was supported by grant STO414/2-4 of the Deutsche Forschungsgemeinschaft, the EuroDEEP program of the European Science Foundation under 06-EuroDEEP-FP-004 MIDDLE project and NSF-grant MCB-0348341 VE wishes to acknowledge Dr. Hilary Morrison and Rich Fox of the Marine Biological Laboratory, Woods Hole for the development and adaptation of their pipeline scripts for processing the sequence data for this study. We thank Linda Woodard for overseeing the richness calculations. This research was conducted using the resources of the Cornell University Center for Advanced Computing, which receives funding from Cornell University, New York State, the National Science Foundation, and other leading public agencies, foundations, and corporations. We thank the captain and the crew of RV Urania for their expert handling of our casts and equipment and for highly productive oceanographic cruises.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by H. Santos.
Rights and permissions
About this article
Cite this article
Edgcomb, V., Orsi, W., Leslin, C. et al. Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea. Extremophiles 13, 151–167 (2009). https://doi.org/10.1007/s00792-008-0206-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-008-0206-2