Microbial Ecology

, Volume 56, Issue 1, pp 168–177 | Cite as

Fungi and Macroaggregation in Deep-Sea Sediments

  • Samir Damare
  • Chandralata Raghukumar
Original Article


Whereas fungi in terrestrial soils have been well studied, little is known of them in deep-sea sediments. Recent studies have demonstrated the presence of fungal hyphae in such sediments but in low abundance. We present evidence in this study that one of the apparent reasons for the poor detection of fungi in deep-sea sediments is their cryptic presence in macroaggregates. Fungal biomass carbon from different core sections of deep-sea sediments from ∼5000 m depth in the Central Indian Ocean was estimated based on direct microscopic detection of fungal mycelia. Treatment of sediment samples with ethylenediamine tetra-acetic acid (EDTA) enabled more frequent detection and significantly higher biomass than in samples without such treatment. Treatment with EDTA resulted in detecting various stages of breakdown of aggregates in the sediments, gradually revealing the presence of fungal hyphae within them. Experimental studies of a deep-sea, as well as three terrestrial isolates of fungi, showed that all could grow at 200 bar and 5°C in a nutrient medium and in deep-sea sediment extract. Hyphae of fungi grown in sediment extract under the above conditions showed various stages of accretion of particles around them, leading to the formation of aggregates. Such aggregates showed the presence of humic material, carbohydrate, and proteins. We suggest that fungi in deep-sea sediments may be involved in humic aggregate formation by processes very similar to those in terrestrial sediments. The importance of such a process in carbon sequestration and food web in the deep sea needs to be examined.


Fungal Biomass Dissolve Organic Matter Fungal Hypha Total Organic Carbon Content Microbial Type Culture Collection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The first author wishes to thank the Council for Scientific and Industrial Research, New Delhi for a senior research fellowship. The corresponding author acknowledges the Department of Biotechnology, New Delhi for the research grant No. BT/PR 1193/AAQ/03/102/2000. This paper has benefited immensely from suggestions made by Dr. S. Raghukumar, and we are grateful for his valuable comments. This is NIO’s contribution No. 4307.


  1. 1.
    Ametzketa E (1999) Soil aggregates stability: a review. J Sustain Agric 14:83–151CrossRefGoogle Scholar
  2. 2.
    Aspiras RB, Allen ON, Harris RF, Chester G (1971) Aggregate stabilization by filamentous microorganisms. Soil Sci 112:282–284CrossRefGoogle Scholar
  3. 3.
    Bailey VL, Smith JL, Bolton H Jr (2002) Fungal-to-bacterial ratios investigated for enhanced C sequestration. Soil Biol Biochem 34:997–1007CrossRefGoogle Scholar
  4. 4.
    Beare MH, Cabrera ML, Hendrix PF, Coleman DC (1994) Aggregate-protected and unprotected pools of organic matter in conventional and no-tillage soils. Soil Sci Soc Am J 58:787–795CrossRefGoogle Scholar
  5. 5.
    Beare MH, Hu S, Coleman DC, Hendrix PF (1997) Influences of mycelial fungi on soil aggregation and organic matter storage in conventional and no-tillage soils. Appl Soil Ecol 5:211–219CrossRefGoogle Scholar
  6. 6.
    Bhaskar PV, Grossart HP, Bhosle NB, Simon M (2005) Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin. FEMS Microb Ecol 53:255–264CrossRefGoogle Scholar
  7. 7.
    Boetius A, Lochte K (2000) Regional variation of total microbial biomass in sediments of the deep Arabian Sea. Deep-Sea Res Part 2 47:149–168CrossRefGoogle Scholar
  8. 8.
    Bronick CJ, Lal R (2005) Soil structure and management: a review. Geoderma 124:3–22CrossRefGoogle Scholar
  9. 9.
    Burns RG (1977) Soil enzymology. Sci Prog (Lond) 64:275–285Google Scholar
  10. 10.
    Burns RG (1978) Enzymes in soil: some theoretical and practical considerations. In: Burns RG (ed) Soil Enzymes, Academic, London, pp 295–339Google Scholar
  11. 11.
    Burns RG, Davies JA (1986) The microbiology of soil structure. In: Lopez-Real JM, Hodges RD (eds) The Role of Microorganisms in a Sustainable Agriculture. A. B. Academic Publishers, Berkhamstead, UK, pp 9–28Google Scholar
  12. 12.
    Chiu CY, Chen TH, Imberger K, Tian G (2006) Particle size fractionation of fungal and bacterial biomass in subalpine grassland and forest soils. Geoderma 130:265–271CrossRefGoogle Scholar
  13. 13.
    Damare S (2007) Deep-sea fungi: occurrence and adaptations. PhD Thesis, Goa University, pp 8.7–8.8Google Scholar
  14. 14.
    Damare S, Raghukumar C, Raghukumar S (2006) Fungi in deep-sea sediments of the Central Indian Basin. Deep-Sea Res Part I 53:14–27CrossRefGoogle Scholar
  15. 15.
    Domsch KH, Gams W, Anderson T-H (1980) Compendium of Soil Fungi. Academic, LondonGoogle Scholar
  16. 16.
    Ekelund F, Rønn R, Christensen S (2001) Distribution with depth of protozoa, bacteria and fungi in soil profiles from three Danish forest sites. Soil Biol Biochem 33:475–481CrossRefGoogle Scholar
  17. 17.
    Elliot ET (1986) Aggregate structure and carbon, nitrogen, and phosphorous in native and cultivated soils. Soil Sci Soc Am J 50:627–633CrossRefGoogle Scholar
  18. 18.
    Filip Z, Haider K (1972) Influence of clay minerals on growth and metabolic activity of Epicoccum nigrum and Stachybotrys chartarum. Soil Biol Biochem 4:135–145CrossRefGoogle Scholar
  19. 19.
    Gunde-Cimermann N, Sonjak S, Zalar P, Frisvad JC, Diderichsen B, Plemenitas A (2003) Extremophilic fungi in arctic ice: a relationship between adaptation to low temperature and water activity. Phys Chem Earth 28:1273–1278Google Scholar
  20. 20.
    Gupta VVSR, Germida JJ (1988) Distribution of microbial biomass and its activity in different soil aggregate size classes as affected by cultivation. Soil Biol Biochem 20:777–786CrossRefGoogle Scholar
  21. 21.
    Ingole BS, Ansari ZA, Rathod V, Rodrigues N (2001) Response of deep-sea macrobenthos to a small-scale environmental disturbance. Deep-Sea Res Part II 48:3401–3410CrossRefGoogle Scholar
  22. 22.
    Kandeler E, Stemmer M, Klimanek EM (1999) Response of soil microbial biomass, urease and xylanase within particle-size fractions to long-term soil management. Soil Biol Biochem 31:261–273CrossRefGoogle Scholar
  23. 23.
    Khadge NH (2000) Geotechnical properties of surface sediments in the INDEX area. Mar Georesour Geotechnol 18:251–258CrossRefGoogle Scholar
  24. 24.
    Klein DA, Paschke MW (2000) A soil community structural-functional index: the microscopy-based total/active/fungal/bacterial (TA/AFB) biovolumes ratio. Appl Soil Ecol 14:257–268CrossRefGoogle Scholar
  25. 25.
    Long RA, Azam F (1996) Abundant protein containing particles in the sea. Aquat Microb Ecol 10:213–221CrossRefGoogle Scholar
  26. 26.
    Lysnes K, Thorseth IH, Steinsbu BO, Øvreås L, Torsvik T, Pedersen RB (2004) Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microb Ecol 50:213–230CrossRefGoogle Scholar
  27. 27.
    Molope MB, Page ER (1986) The contributions of fungi, bacteria and physical processes in the development of aggregate stability of a cultivated soil. In: Lopez-Real JM, Hodges RD (eds) The Role of Microorganisms in a Sustainable Agriculture. A.B. Academic Publishers, Berkhamstead, UK, ppGoogle Scholar
  28. 28.
    Moreira D, Lopez-Garcia P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 101:31–38Google Scholar
  29. 29.
    Okada H, Kadota I (2003) Host status of 10 fungal isolates for two nematode species, Filenchus misellus and Aphelenchus avenae. Soil Biol Biochem 35:1601–1607CrossRefGoogle Scholar
  30. 30.
    Okada H, Harada H, Kadota I (2005) Fungal-feeding habits of six nematode isolates in the genus Filenchus. Soil Biol Biochem 37:1113–1120CrossRefGoogle Scholar
  31. 31.
    Parulekar AH, Harkantra SN, Ansari ZA, Matondkar SGP (1982) Abyssal benthos of the Central Indian Ocean. Deep-Sea Res. A 12:1531–1537CrossRefGoogle Scholar
  32. 32.
    Raghukumar C, Raghukumar S, Sharma S, Chandramohan D (1992) Endolithic fungi from deep-sea calcareous substrata: isolation and laboratory studies. In: Desai BN (ed) Oceanography of the Indian Ocean, Oxford & IBH, New Delhi, pp 3–9Google Scholar
  33. 33.
    Raghukumar C, Raghukumar S, Sheelu G, Gupta SM, Nagender Nath B, Rao BR (2004) Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench, Indian Ocean. Deep-Sea Res Part I 51:1759–1768Google Scholar
  34. 34.
    Shankar R, Subbarao KV, Kolla V (1987) Geochemistry of surface sediments from the Arabian Sea. Mar Geol 76:253–279CrossRefGoogle Scholar
  35. 35.
    Sharma R, Nath BN, Parthiban G, Jai Sankar S (2001) Sediment redistribution during simulated benthic disturbance and its implications on deep seabed mining. Deep-Sea Res Part II 48:3363–3380CrossRefGoogle Scholar
  36. 36.
    Sharma R, Nath BN (2005) Benthic environmental variability in the Central Indian Basin-I, Technical Report, pp 118Google Scholar
  37. 37.
    Sieberth JM, Julseth A (1968) Studies on algal substances in the sea I. Gelbstoff (Humic material) in terrestrial and marine waters. J Exp Mar Biol Ecol 2:174–189CrossRefGoogle Scholar
  38. 38.
    Stevenson (1982) Jerzy Weber’s Homepage. The Formation of Humic Substances.
  39. 39.
    Suberkropp K, Meyers H (1996) Application of fungal and bacterial production methodologies to decomposing leaves in streams. Appl Environ Microbiol 62:1610–1615PubMedGoogle Scholar
  40. 40.
    Takami H, Kobata K, Nagahama T, Kobayashi H, Horikoshi K (1999) Biodiversity in deep-sea sites near the south part of Japan. Extremophiles 3:91–102Google Scholar
  41. 41.
    Tisdall JM, Oades JM (1982) Organic matter and water-stable aggregates in soils. J Soil Sci 33:141–163CrossRefGoogle Scholar
  42. 42.
    Valsangkar AB, Ambre NV (2000) Distribution of grain size and clay minerals in sediments from the INDEX area, Central Indian Basin. Mar Georesour Geotec 18:189–199CrossRefGoogle Scholar
  43. 43.
    Vanucci S, Dell’Anno A, Pusceddu A, Fabiano M, Lampitt RS, Danovaro R (2001) Microbial assemblages associated with sinking particles in the Porcupine Abyssal Plain (NE Atlantic Ocean). Prog Oceanogr 50:105–121CrossRefGoogle Scholar
  44. 44.
    Van veen JA, Paul EA (1979) Conversion of biovolume measurements of soil organisms, grown under various moisture tensions, to biomass and their nutrient content. Appl Environ Microbiol 37:686–692PubMedGoogle Scholar
  45. 45.
    Verdugo P, Alldredge AL, Azam F, Kirchman DL, Passow U, Antschi PH (2004) The oceanic gel phase: a bridge in the DOM-POM continuum. Mar Chem 92:67–85CrossRefGoogle Scholar
  46. 46.
    Vieira FCS, Nahas E (2005) Comparison of microbial numbers in soils using various culture media and temperatures. Microbiol Res 160:197–202PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.National Institute of OceanographyDona PaulaIndia

Personalised recommendations