Skip to main content

Advertisement

SpringerLink
Log in

Isolation and characterisation of bacteria from the Eastern Mediterranean deep sea

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

The Eastern Mediterranean deep sea is one of the most oligotrophic regions in the world’s ocean. With the aim to classify bacteria from this special environment we isolated 107 strains affiliating to the Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria and Bacteroidetes from sediments of the Eastern Mediterranean Sea. As determined by 16S rRNA gene sequence analysis, Actinobacteria and Firmicutes, in particular members of the genus Bacillus, were dominant and represented a remarkable diversity with 27 out of a total of 33 operational taxonomic units obtained from the untreated sediment. The considerable percentage of operational taxonomic units (42%) which may be considered to be new species underlines the uniqueness of the studied environment. In order to selectively enrich bacteria which are adapted to the deep-sea conditions and tolerate broad pressure ranges, enrichments were set up with a sediment sample under in situ pressure and temperature (28 MPa, 13.5°C) using N-acetyl-d-glucosamine as substrate. Interestingly Gammaproteobacteria were significantly enriched and dominant among the strains isolated after pressure pre-incubation. Obviously, Gammaproteobacteria have a selective advantage under the enrichment conditions applied mimicking nutrient supply under pressure conditions and cope well with sudden changes of hydrostatic pressure. However, under the continued low nutrient situation in the Eastern Mediterranean deep-sea sediments apparently Firmicutes and Actinobacteria have a clear adaptative advantage.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Bianchi A, Garcin J, Tholosan O (1999) A high-pressure serial sampler to measure microbial activity in the deep sea. Deep-Sea Res Part I 46:2129–2142

    Article  Google Scholar 

  • Carlucci AF, Shimp SL, Craven DB (1986) Growth characteristics of low-nutrient bacteria from the north-east and central Pacific Ocean. FEMS Microbiol Lett 38:1–10

    Article  CAS  Google Scholar 

  • Carrigg C, Rice O, Kavanagh S, Collins G, O′Flaherty V (2007) DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 77:955–964

    Article  PubMed  CAS  Google Scholar 

  • Chastain RA, Yayanos AA (1991) Ultrastructural changes in an obligately barophilic marine bacterium after decompression. Appl Environ Microbiol 57:1489–1497

    PubMed  CAS  Google Scholar 

  • Colquhoun JA, Heald SC, Li L, Tamaoka J, Kato C, Horikoshi K, Bull AT (1998) Taxonomy and biotransformation activities of some deep-sea actinomycetes. Extremophiles 2:269–277

    Article  PubMed  CAS  Google Scholar 

  • D’ Hondt S, Jorgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, Cypionka H, Dickens GR, Ferdelman T, Hinrichs KU (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306:2216–2221

    Article  PubMed  Google Scholar 

  • Danovaro R, Marrale D, Dell’ Anno A (2000) Bacterial response to seasonal changes in labile organic matter composition on the continental shelf and bathyal sediments of the Cretan Sea. Prog Oceanogr 46:345–366

    Article  Google Scholar 

  • Danovaro R, Corinaldesi C, Luna GM, Magagnini M, Manini E, Pusceddu A (2009) Prokaryote diversity and viral production in deep-sea sediments and seamounts. Deep Sea Res Part II 56:738–747

    Article  Google Scholar 

  • Das S, Lyla PS, Khan SA (2006) Marine microbial diversity and ecology: importance and future perspectives. Cur Sci 90:1325–1335

    CAS  Google Scholar 

  • Delong EF, Franks DG, Yayanos AA (1997) Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol 63:2105–2108

    PubMed  CAS  Google Scholar 

  • Dick GJ, Lee YE, Tebo BM (2006) Manganese (II)-oxidizing Bacillus spores in Guaymas basin hydrothermal sediments and plumes. Appl Environ Microbiol 72:3184

    Article  PubMed  CAS  Google Scholar 

  • Emig C, Geistdoerfer P (2004) The Mediterranean deep-sea fauna: historical evolution, bathymetric variations and geographical changes. Carnets de Geologie/Netbooks on Geology, Article 2004/01 (CG2004_A01_CCE-PG)

  • Fuchs BM, Zubkov MV, Sahm K, Burkill PH, Amann R (2000) Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Environ Microbiol 2:191–201

    Article  PubMed  CAS  Google Scholar 

  • Gärtner A, Wiese J, Imhoff JF (2008) Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field. Int J Syst Evol Microbiol 58:34–39

    Article  PubMed  Google Scholar 

  • Gontang EA, Fenical W, Jensen PR (2007) Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73:3272–3282

    Article  PubMed  CAS  Google Scholar 

  • Gooday GW (1990) Physiology of microbial degradation of chitin and chitosan. Biodegradation 1:177–190

    Article  CAS  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  • Heijs SK, Laverman AM, Forney LJ, Hardoim PR, van Elsas JD (2008) Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol 64:362–377

    Article  PubMed  CAS  Google Scholar 

  • Hoi LT, Voigt B, Jürgen B, Ehrenreich A, Gottschalk G, Evers S, Feesche J, Maurer KH, Hecker M, Schweder T (2006) The phosphate starvation response of Bacillus licheniformis. Proteomics 6:3582–3601

    Article  CAS  Google Scholar 

  • Ivanova EP, Vysotskii MV, Svetashev VI, Nedashkovskaya OI, Gorshkova NM, Mikhailov VV, Yumoto N, Shigeri Y, Taguchi T, Yoshikawa S (1999) Characterization of Bacillus strains of marine origin. Int Microbiol 2:267–271

    PubMed  CAS  Google Scholar 

  • Jannasch HJ, Wirsen CO, Taylor CD (1976) Undecompressed microbial populations from the deep sea. Appl Environ Microbiol 32:360–367

    PubMed  CAS  Google Scholar 

  • Jensen PR, Gontang E, Mafnas C, Mincer TJ, Fenical W (2005) Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ Microbiol 7:1039–1048

    Article  PubMed  Google Scholar 

  • Kato C, Sato T, Horikoshi K (1995) Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples. Biodivers Conserv 4:1–9

    Article  Google Scholar 

  • Kato C, Inoue A, Horikoshi K (1996) Isolating and characterizing deep-sea marine microorganisms. Trends Biotechnol 14:6–12

    Article  PubMed  CAS  Google Scholar 

  • Kato C, Li L, Nogi Y, Nakamura Y, Tamaoka J, Horikoshi K (1998) Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Appl Environ Microbiol 64:1510–1513

    PubMed  CAS  Google Scholar 

  • Kato C, Yanagibayashi M, Nogi Y, Horikoshi K (1999) Analyses of microbial diversity in the sediment obtained from Japan Trench at a depth of 7326 m and high pressure cultivation. JAMAREC J Deep Sea Res Biol 15:47–52

    Google Scholar 

  • Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6:29. doi:10.1186/1471-2148-6-29

    Article  PubMed  Google Scholar 

  • Koch AL (2001) Oligotrophs versus copiotrophs. Bioassays 23:657–661

    Article  CAS  Google Scholar 

  • Koepke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819–7830

    Article  CAS  Google Scholar 

  • Kontoyiannis H, Theocharis A, Balopoulos E, Kioroglou S, Papadopoulos V, Collins M, Velegrakis AF, Iona A (1999) Water fluxes through the cretan arc straits, Eastern Mediterranean Sea: March 1994 to June 1995. Prog Oceanogr 44:511–529

    Article  Google Scholar 

  • Lampadariou N, Tselepides A, Hatziyanni E (2009) Deep-sea meiofaunal and foraminiferal communities along a gradient of primary productivity in the eastern Mediterranean Sea. Scientia Marina 73:337–345

    Article  Google Scholar 

  • Lampitt RS, Antia AN (1997) Particle flux in deep seas: regional characteristics and temporal variability. Deep Sea Res Part I 44:1377–1403

    Article  CAS  Google Scholar 

  • Lauro FM, Bartlett DH (2008) Prokaryotic lifestyles in deep sea habitats. Extremophiles 12:15–25

    Article  PubMed  Google Scholar 

  • Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH (2007) The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol 73:838–845

    Article  PubMed  CAS  Google Scholar 

  • Li L, Guenzennec J, Nichols P, Henry P, Yanagibayashi M, Kato C (1999a) Microbial diversity in Nankai trough sediments at a depth of 3843 m. J Oceanogr 55:635–642

    Article  CAS  Google Scholar 

  • Li L, Kato C, Horikoshi K (1999b) Bacterial diversity in deep-sea sediments from different depths. Biodivers Conserv 8:659–677

    Article  Google Scholar 

  • Lopez-Lopez A, Bartual SG, Stal L, Onyshchenko O, Rodriguez-Valera F (2005) Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea. Environ Microbiol 7:649–659

    Article  PubMed  CAS  Google Scholar 

  • Ludwig W (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  PubMed  CAS  Google Scholar 

  • Luna GM, Dell’ Anno A, Giuliano L, Danovaro R (2004) Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability. Environ Microbiol 6:745–753

    Article  PubMed  CAS  Google Scholar 

  • Marteinsson VT, Birrien JL, Jeanthon C, Prieur D (1996) Numerical taxonomic study of thermophilic Bacillus isolated from three geographically separated deep-sea hydrothermal vents. FEMS Microbiol Ecol 21:255–266

    Article  CAS  Google Scholar 

  • Martin-Cuadrado AB, Ghai R, Gonzaga A, Rodriguez-Valera F (2009) CO Dehydrogenase genes found in metagenomic fosmid clones from the Deep Mediterranean Sea. Appl Environ Microbiol 75:7436–7444

    Article  PubMed  CAS  Google Scholar 

  • McVeigh HP, Munro J, Embley TM (1996) Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J Ind Microb Biotech 17:197–204

    Article  CAS  Google Scholar 

  • Mincer TJ, Fenical W, Jensen PR (2005) Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl Environ Microbiol 71:7019–7028

    Article  PubMed  CAS  Google Scholar 

  • Pagan R, Mackey B (2000) Relationship between membrane damage and cell death in pressure-treated Escherichia coli cells: differences between exponential-and stationary-phase cells and variation among strains. Appl Environ Microbiol 66:2829–2834

    Article  PubMed  CAS  Google Scholar 

  • Park CB, Clark DS (2002) Rupture of the cell envelope by decompression of the deep-sea methanogen Methanococcus jannaschii. Appl Environ Microbiol 68:1458–1463

    Article  PubMed  CAS  Google Scholar 

  • Pathom-aree W, Stach J, Ward A, Horikoshi K, Bull A, Goodfellow M (2006) Diversity of actinomycetes isolated from Challenger deep sediment (10.898 m) from the Mariana trench. Extremophiles 10:181–189

    Article  PubMed  CAS  Google Scholar 

  • Pinhassi J, Berman T (2003) Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the Eastern Mediterranean Sea, and the Gulf of Eilat. Appl Environ Microbiol 69:199–211

    Article  PubMed  CAS  Google Scholar 

  • Polymenakou PN, Lampadariou N, Tselepides A (2008) Exo-enzymatic activities and organic matter properties in deep-sea canyon and slope systems off the southern Cretan margin. Deep-Sea Res Part 1 55:1318–1329

    Article  CAS  Google Scholar 

  • Polymenakou PN, Lampadariou N, Mandalakis M, Tselepides A (2009) Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Syst Appl Microbiol 32:17–26

    Article  PubMed  CAS  Google Scholar 

  • Prieto-Davó A, Fenical W, Jensen PR (2008) Comparative actinomycete diversity in marine sediments. Aquat Microb Ecol 52:1–11

    Article  Google Scholar 

  • Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (1999) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  Google Scholar 

  • Rosson RA, Nealson KH (1982) Manganese binding and oxidation by spores of a marine bacillus. J Bacteriol 151:1027–1034

    PubMed  CAS  Google Scholar 

  • Rueger HJ, Tan TL (1992) Community structures of cold and low-nutrient adapted heterotrophic sediment bacteria from the deep eastern tropical Atlantic. Mar Ecol Prog Ser 84:83–93

    Article  Google Scholar 

  • Rueger HJ, Fritze D, Sproer C (2000) New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species. Int J Syst Evol Microbiol 50:1305–1313

    Article  Google Scholar 

  • Seki H, Robinson DG (1969) Effect of decompression on activity of microorganisms in seawater. Internationale Revue der gesamten Hydrobiologie und Hydrographie 54:201–205

    Article  Google Scholar 

  • Siefert JL, Larios-Sanz M, Nakamura LK, Slepecky RA, Paul JH, Moore ERB, Fox GE, Jurtshuk J (2000) Phylogeny of marine Bacillus isolates from the Gulf of Mexico. Curr Microbiol 41:84–88

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  • Stevens H, Brinkhoff T, Rink B, Vollmers J, Simon M (2007) Diversity and abundance of Gram-positive bacteria in a tidal flat ecosystem. Environ Microbiol 9:1810–1822

    Article  PubMed  CAS  Google Scholar 

  • Süß J, Engelen B, Cypionka H, Sass H (2004) Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods. FEMS Microbiol Ecol 51:109–121

    Article  PubMed  Google Scholar 

  • Takami H, Inoue A, Fuji F, Horikoshi K (1997) Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiol Lett 152:279–285

    Article  PubMed  CAS  Google Scholar 

  • Yanagibayashi M, Nogi Y, Li L, Kato C (1999) Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol Lett 170:271–279

    Article  PubMed  CAS  Google Scholar 

  • Yayanos AA, Dietz AS, Van Boxtel R (1979) Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 205:808–810

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank the captain and crew of RV Meteor as well as the scientific party of M71/2 for any support during the cruise. We are grateful to Dr. Jörg Süling for onboard support and fruitful discussion. We thank the colleagues from the IKMB (Institute of Clinical Molecular Biology) in Kiel (Germany) for sequencing. We are also thankful for the valuable suggestions of the unknown reviewers. This work was supported by a grant of the Deutsche Forschungsgemeinschaft and the Kieler Wirkstoff-Zentrum am IFM-GEOMAR granted by the Ministry of Science, Economic Affaires and Transport of the State of Schleswig–Holstein (Germany) in the frame of “Future Program for Economy” which is co-financed by EFRE.

Author information

Authors and Affiliations

  1. Kieler Wirkstoff-Zentrum am IFM-GEOMAR, Am Kiel-Kanal 44, 24106, Kiel, Germany

    Andrea Gärtner, Martina Blümel, Jutta Wiese & Johannes F. Imhoff

  2. Leibniz-Institut für Meereswissenschaften IFM-GEOMAR, Düsternbrooker Weg 20, 24105, Kiel, Germany

    Johannes F. Imhoff

Authors
  1. Andrea Gärtner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martina Blümel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jutta Wiese
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Johannes F. Imhoff
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Johannes F. Imhoff.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10482_2011_9599_MOESM1_ESM.png

Supplementary material 1 Total number of strains obtained from the two sampling sites (Ierapetra Basin (IB), 4400m and Herodotos Plain (HP), 2800 m) and their phylogenetic affiliation compared to the pressurised sediment enrichment (PNG 6 kb)

10482_2011_9599_MOESM2_ESM.png

Supplementary material 2 Number of unique and shared OTUs from the water (n = 12), the sediment (n = 33) and the pressurised sediment enrichment (n = 15) (PNG 26 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gärtner, A., Blümel, M., Wiese, J. et al. Isolation and characterisation of bacteria from the Eastern Mediterranean deep sea. Antonie van Leeuwenhoek 100, 421–435 (2011). https://doi.org/10.1007/s10482-011-9599-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-011-9599-5

Keywords

Search

Navigation