Skip to main content
Log in

Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation

  • SOIL BIOLOGY
  • Published:
Eurasian Soil Science Aims and scope Submit manuscript

Abstract

Bacteria play a crucial role in regulating biogeochemical cycles in peatlands. Most of the studies on soil bacteria focus mainly on the peat surface and bacteria that exist in the deeper peat layers are still poorly known in tropical areas. This study was conducted to examine bacterial abundances along the peat depths in peat forest ecosystems (peat swamp forest (PSF) and logged-over secondary forest (LOF)) and an oil palm plantation (7.5 years after planting (7.5 YAP OPP)) at intervals of 0–30 cm, 30–40 cm, 40–50 cm, and 50–60 cm. Isolation of bacteria from peat samples was carried out on several selective and non-selective media. Bacteria identification was conducted by amplifying the 16S rRNA gene. The result showed that the same dominant bacterial taxa were found with different abundances in all study sites which were Proteobacteria, Firmicutes, and Actinobacteria. Vertical stratification of Proteobacteria and Firmicutes was observed along the depths, might due to the fluctuations of water table in the peatland mainly in 7.5 YAP OPP. Richness was highest at 0–30 cm in LOF and 7.5 YAP OPP, while PSF at 30–40 cm. This study suggests that deeper peat depth supports the bacterial growth and environmental conditions related to water table level influenced the bacterial abundances.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1.
Fig. 2.

Similar content being viewed by others

REFERENCES

  1. R. Andersen, S. J. Chapman, and R. R. E. Artz, “Microbial communities in natural and disturbed peatlands: a review,” Soil Biol. Biochem. 57, 979–994 (2013). https://doi.org/10.1016/j.soilbio.2012.10.003

    Article  Google Scholar 

  2. B. F. Azadeh, M. Sariah, and M. Y. Wong, “Characterization of Burkholderia cepacia genomovar I as a potential biocontrol agent of Ganoderma boninense in oil palm,” Afr. J. Biotechnol. 9, 3542–3548 (2010).

    Google Scholar 

  3. S. Bardhan, S. Jose, M. A. Jenkins, C. R. Webster, R. P. Udawatta, and S. E. Stehn, “Microbial community diversity and composition across a gradient of soil acidity in spruce–fir forests of the southern Appalachian Mountains,” Appl. Soil Ecol. 61, 60–68 (2012). https://doi.org/10.1016/j.apsoil.2012.04.010

    Article  Google Scholar 

  4. L. Canfora, G. Bacci, F. Pinzari, G. Lo Papa, C. Dazzi, and A. Benedetti, “Salinity and bacterial diversity: to what extent does the concentration of salt affect the bacterial community in a saline soil?” PLoS One 9, e106662 (2014). https://doi.org/10.1371/journal.pone.0106662

    Article  Google Scholar 

  5. K. E. R. Davis, S. J. Joseph, and P. H. Janssen, “Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria,” Appl. Environ. Microbiol. 71, 826–834 (2005). https://doi.org/10.1128/AEM.71.2.826

    Article  Google Scholar 

  6. T. G. Dobrovol’skaya, D. G. Zvyagintsev, I. Y. Chernov, A. V Golovchenko, G. M. Zenova, L. V. Lysak, N. A. Manucharova, O. E. Marfenina, L. M. Polyanskaya, A. L. Stepanov, and M. M. Umarov, “The role of microorganisms in the ecological functions of soils,” Eurasian Soil Sci. 48, 959–967 (2015). https://doi.org/10.1134/S1064229315090033

    Article  Google Scholar 

  7. D. R. Elliott, S. J. M. Caporn, F. Nwaishi, R. H. Nilsson, and R. Sen, “Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation,” PLoS One 10, e0124726 (2015). https://doi.org/10.1371/journal.pone.0124726

    Article  Google Scholar 

  8. N. Fierer, “Embracing the unknown: disentangling the complexities of the soil microbiome,” Nat. Rev. Microbiol. 15, 579–590 (2017). https://doi.org/10.1038/nrmicro.2017.87

    Article  Google Scholar 

  9. N. Fierer, M. A. Bradford, and R. B. Jackson, “Towards an ecological classification of soil bacteria,” Ecology 88, 1354–1364 (2007). https://doi.org/10.1007/s00209-018-2115-0

    Article  Google Scholar 

  10. N. Fierer, J. P. Schimel, and P. A. Holden, “Variations in microbial community composition through two soil depth profiles,” Soil Biol. Biochem. 35, 167–176 (2003). https://doi.org/10.1016/S0038-0717(02)00251-1

    Article  Google Scholar 

  11. J. J. Germida and J. R. De Freitas, “Cultural methods for soil and root-associated microorganisms,” in Soil Sampling and Methods of Analysis, Ed. by M. R. Carter and E. G. Gregorich (CRC Press, Boca Raton, 2007), pp. 341–354.

    Google Scholar 

  12. A. Ghazali, S. Asmah, M. Syafiq, M. S. Yahya, N. Aziz, T. Peng, A. R. Norhisham, C. Leong, E. C. Turner, and B. Azhar, “Effects of monoculture and polyculture farming in oil palm smallholdings on terrestrial arthropod diversity,” J. Asia-Pac. Entomol. 19, 415–421 (2016). https://doi.org/10.1016/j.aspen.2016.04.016

    Article  Google Scholar 

  13. C. M. Hansel, S. Fendorf, P. M. Jardine, and C. A. Francis, “Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile,” Appl. Environ. Microbiol. 74, 1620–1633 (2008). https://doi.org/10.1128/AEM.01787-07

    Article  Google Scholar 

  14. W. F. Harrigan and M. E. McCance, Laboratory Methods in Microbiology (Academic, London, 1966).

    Google Scholar 

  15. K. Holland, J. S. Knapp, and J. Shoesmith, Anaerobic Bacteria (Blackie, London, 1987).

    Book  Google Scholar 

  16. E. B. Hollister, A. S. Engledow, A. J. M. Hammett, T. L. Provin, H. H. Wilkinson, and T. J. Gentry, “Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments,” ISME J. 4, 829–838 (2010). https://doi.org/10.1038/ismej.2010.3

    Article  Google Scholar 

  17. B. Hu, D. Rush, E. van der Biezen, P. Zheng, M. van Mullekom, S. Schouten, J. S. S. Damste, A. J. P. Smolders, M. S. M. Jetten, and B. Kartal, “New anaerobic, ammonium-oxidizing community enriched from peat soil,” Appl. Environ. Microbiol. 77, 966–971 (2011). https://doi.org/10.1128/AEM.02402-10

    Article  Google Scholar 

  18. X. Hu, J. Chen, and J. Guo, “Two phosphate- and potassium-solubilizing bacteria isolated from Tianmu Mountain, Zhejiang, China,” World J. Microbiol. Biotechnol. 22, 983–990 (2006). https://doi.org/10.1007/s11274-006-9144-2

    Article  Google Scholar 

  19. L. M. Irenge and J. Gala, “Rapid detection methods for Bacillus anthracis in environmental samples: a review,” Appl. Microbiol. Biotechnol. 93, 1411–1422 (2012). https://doi.org/10.1007/s00253-011-3845-7

    Article  Google Scholar 

  20. A. A. Ivanova, C. Wegner, Y. Kim, W. Liesack, and S.N. Dedysh, “Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis,” Mol. Ecol. 25, 4818–4835 (2016). https://doi.org/10.1111/mec.13806

    Article  Google Scholar 

  21. K. Jaatinen, R. Laiho, A. Vuorenmaa, U. del Castillo, K. Minkkinen, T. Pennanen, T. Penttilä, and H. Fritze, “Responses of aerobic microbial communities and soil respiration to water-level drawdown in a northern boreal fen,” Environ. Microbiol. 10, 339–353 (2008). https://doi.org/10.1111/j.1462-2920.2007.01455.x

    Article  Google Scholar 

  22. C. R. Jackson, K. C. Liew, and C. M. Yule, “Structural and functional changes with depth in microbial communities in a tropical Malaysian peat swamp forest,” Microb. Ecol. 57, 402–412 (2009). https://doi.org/10.1007/s00248-008-9409-4

    Article  Google Scholar 

  23. J. K. Jansson and N. Tas, “The microbial ecology of permafrost,” Nat. Rev. Microbiol. 12, 414–425 (2014). https://doi.org/10.1038/nrmicro3262

    Article  Google Scholar 

  24. K. Karagöz, F. Ates, H. Karagöz, R. Kotan, and R. Cakmakci, “Characterization of plant growth-promoting traits of bacteria isolated from the rhizosphere of grapevine grown in alkaline and acidic soils,” Eur. J. Soil Biol. 50, 144–150 (2012). https://doi.org/10.1016/j.ejsobi.2012.01.007

    Article  Google Scholar 

  25. S. Kim, C. Freeman, N. Fenner, and H. Kang, “Functional and structural responses of bacterial and methanogen communities to 3-year warming incubation in different depths of peat mire,” Appl. Soil Ecol. 57, 23–30 (2012). https://doi.org/10.1016/j.apsoil.2012.02.015

    Article  Google Scholar 

  26. Y. Kim, S. Lee, Y. Cho, H. Oh, and Y. H. Ko, “Isolation of cellulolytic Bacillus subtilis strains from agricultural environments,” ISRN Microbiol. 2012, 1–9 (2012). https://doi.org/10.5402/2012/650563

    Article  Google Scholar 

  27. M. M. Kotowska, C. Leuschner, T. Triadiati, S. Meriem, and D. Hertel, “Quantifying above- and belowground biomass carbon loss with forest conversion in tropical lowlands of Sumatra (Indonesia),” Glob. Chang. Biol. 21, 3620–3634 (2015). https://doi.org/10.1111/gcb.12979

    Article  Google Scholar 

  28. N. A. Kusai, Z. Ayob, M. S. T. Maidin, S. Safari, and S. R. Ahmad Ali, “Characterization of fungi from different ecosystems of tropical peat in Sarawak, Malaysia,” Rend. Lincei. Sci. Fis. Nat. 29, 469–482 (2018). https://doi.org/10.1007/s12210-018-0685-8

    Article  Google Scholar 

  29. C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, “Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale,” Appl. Environ. Microbiol. 75, 5111–5120 (2009). https://doi.org/10.1128/AEM.00335-09

    Article  Google Scholar 

  30. L. Lee-Cruz, D. P. Edwards, B. M. Tripathi, and J. M. Adams, “Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo,” Appl. Environ. Microbiol. 79, 7290–7297 (2013). https://doi.org/10.1128/AEM.02541-13

    Article  Google Scholar 

  31. J. W. Leff, S. E. Jones, S. M. Prober, A. Barberán, E. T. Borer, J. L. Firn, W. S. Harpole, S. E. Hobbie, K. S. Hofmockel, J. M. H. Knops, R. L. McCulley, K. L. Pierre, A. C. Risch, E. W. Seabloom, M. Schutz, et al., “Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe,” Proc. Natl. Acad. Sci. U.S.A. 112, 10967–10972 (2015). https://doi.org/10.1073/pnas.1508382112

    Article  Google Scholar 

  32. X. Lin, S. Green, M. M. Tfaily, O. Prakash, K. T. Konstantinidis, J. E. Corbett, J. P. Chanton, W. T. Cooper, and J. E. Kostka, “Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the glacial,” Appl. Environ. Microbiol. 78, 7023–7031 (2012). https://doi.org/10.1128/AEM.01750-12

    Article  Google Scholar 

  33. X. Lin, M. M. Tfaily, J. M. Steinweg, P. Chanton, K. Esson, Z. K. Yang, J. P. Chanton, W. Cooper, C. W. Schadt, and J. E. Kostka, “Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA,” Appl. Environ. Microbiol. 80, 3518–3530 (2014). https://doi.org/10.1128/AEM.00205-14

    Article  Google Scholar 

  34. B. Ma and J. Gong, “A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils,” World J. Microbiol. Biotechnol. 29, 2325–2334 (2013). https://doi.org/10.1007/s11274-013-1399-9

    Article  Google Scholar 

  35. M. S. T. Maidin, S. Safari, N. A. Ghani, S. A. Syed Ibrahim, S. Ahmad Bakeri, and M. M. Mohd Masri, “Differences in prokaryotic species between primary and logged-over deep peat forest,” J. Oil Palm Res. 28, 281–295 (2016). https://doi.org/10.21894/jopr.2016.2803.05

    Article  Google Scholar 

  36. I. Mandic-Mulec, L. Ausec, T. Danevčič, Š. Levičnik-Höfferle, V. Jerman, and B. Kraigher, “Microbial community structure and function in peat soil,” Food Technol. Biotechnol. 52, 180–187 (2014).

    Google Scholar 

  37. S. Mishra, W. A. Lee, A. Hooijer, S. Reuben, I. M. Sudiana, A. Idris, and S. Swarup, “Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands,” Biogeosciences 11, 1727–1741 (2014). https://doi.org/10.5194/bg-11-1727-2014

    Article  Google Scholar 

  38. G. Muyzer, A. Teske, C. O. Wirsen, and W. J. Holger, “Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments,” Arch. Microbiol. 164, 165–172 (1995). https://doi.org/10.1007/BF02529967

    Article  Google Scholar 

  39. G. Muyzer, E. C. D. E. Waal, and A. G. Uitierlinden, “Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA,” Appl. Environ. Microbiol. 59, 695–700 (1993)

    Article  Google Scholar 

  40. Y. Nurulita, E. M. Adetutu, H. Gunawan, D. Zul, and A. S. Ball, “Restoration of tropical peat soils : The application of soil microbiology for monitoring the success of the restoration process,” Agric. Ecosyst. Environ. 216, 293–303 (2016). https://doi.org/10.1016/j.agee.2015.09.031

    Article  Google Scholar 

  41. F. Oloo, A. Valverde, M. V. Quiroga, S. Vikram, D. Cowan, and G. Mataloni, “Habitat heterogeneity and connectivity shape microbial communities in South American peatlands,” Sci. Rep. 6, 25712 (2016). https://doi.org/10.1038/srep25712

    Article  Google Scholar 

  42. M. Oshiki, H. Satoh, and S. Okabe, “Ecology and physiology of anaerobic ammonium oxidizing bacteria,” Environ. Microbiol. 18, 2784–2796 (2016). https://doi.org/10.1111/1462-2920.13134

    Article  Google Scholar 

  43. S. Paramananthan, Soils of The MPOB’S Biodiversity Project Sites Maludam National Park & Tanjung Batu Forest (Selangor, 2012)

    Google Scholar 

  44. S. Paramananthan, Soils of The MPOB’S Biodiversity Study Area Proposed Cermat Ceria and Durafarm Plantations (Selangor, 2012)

    Google Scholar 

  45. J. N. Porter, J. J. Wilhelm, and H. D. Tresner, “Method for the preferential isolation of actinomycetes from soils,” Appl. Microbiol. 8, 174–178 (1960).

    Article  Google Scholar 

  46. M. D. Preston, K. A. Smemo, J. W. Mclaughlin, and N. Basiliko, “Peatland microbial communities and decomposition processes in the James Bay Lowlands, Canada,” Front. Microbiol. 3, 70 (2012). https://doi.org/10.3389/fmicb.2012.00070

    Article  Google Scholar 

  47. R. J. Rennie, “A single medium for the isolation of acetylene-reducing (dinitrogen-fixing) bacteria from soils,” Can. J. Microbiol. 27, 8–14 (1981). https://doi.org/10.1139/m81-002

    Article  Google Scholar 

  48. L. A. Rojas, C. Yanez, M. Gonzalez, S. Lobos, K. Smalla, and M. Seegar, “Characterization of the metabolically modified heavy metal-resistant Cupriavidus metallidurans strain MSR33 generated for mercury bioremediation,” PLoS One 6, e17555 (2011). https://doi.org/10.1371/journal.pone.0017555

    Article  Google Scholar 

  49. I. Safni, S. Subandiyah, and M. Fegan, “Ecology, epidemiology and disease management of Ralstonia syzygii in Indonesia,” Front. Microbiol. 9, 419 (2018). https://doi.org/10.3389/fmicb.2018.00419

    Article  Google Scholar 

  50. P. Estrada-de Los Santos, N. B. Vacaseydel-Aceves, L. Martínez-Aguilar, M. A. Cruz-Hernández, A. Mendoza-Herrera, and J. Caballero-Mellado, “Cupriavidus and Burkholderia species associated with agricultural plants that grow in alkaline soils,” J. Microbiol. 49, 867–876 (2011). https://doi.org/10.1007/s12275-011-1127-9

    Article  Google Scholar 

  51. Y. M. Serkebaeva, Y. Kim, W. Liesack, and S. N. Dedysh, “Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a Northern Wetland with focus on poorly studied phyla and candidate divisions,” PLoS One 8, e63994 (2013). https://doi.org/10.1371/journal.pone.0063994

    Article  Google Scholar 

  52. S. Shamim and A. Rehman, “Antioxidative enzyme profiling and biosorption ability of Cupriavidus metallidurans CH34 and Pseudomonas putida mt2 under cadmium stress,” J. Basic Microbiol. 53, 374–381 (2013). https://doi.org/10.1002/jobm.201300038

    Article  Google Scholar 

  53. L. Song, D. Gilbert, and D. Wu, “Vertical micro-distribution of microbial communities living in Sphagnum fallax,” Aquat. Microb. Ecol. 77, 1–10 (2016). https://doi.org/10.3354/ame01783

    Article  Google Scholar 

  54. H. Sun, E. Terhonen, K. Koskinen, L. Paulin, R. Kasanen, and F. O. Asiegbu, “Bacterial diversity and community structure along different peat soils in boreal forest,” Appl. Soil Ecol. 74, 37–45 (2014). https://doi.org/10.1016/j.apsoil.2013.09.010

    Article  Google Scholar 

  55. B. M. Tripathi, D. P. Edwards, L. W. Mendes, M. Kim, K. Dong, H. Kim, and J. M. Adams, “The impact of tropical forest logging and oil palm agriculture on the soil microbiome,” Mol. Ecol. 25, 2244–2257 (2016). https://doi.org/10.1111/mec.13620

    Article  Google Scholar 

  56. B. M. Tripathi, M. Kim, Y. Kim, E. Byun, J.-W. Yang, J. Ahn, and Y. K. Lee, “Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores,” Sci. Rep. 8, 1–11 (2018). https://doi.org/10.1038/s41598-017-18777-x

    Article  Google Scholar 

  57. P. Trivedi, M. Delgado-baquerizo, I. C. Anderson, and B. K. Singh, “Response of soil properties and microbial communities to agriculture: implications for primary productivity and soil health indicators,” Front. Plant Sci. 7, 990 (2016). https://doi.org/10.3389/fpls.2016.00990

    Article  Google Scholar 

  58. A. Tveit, R. Schwacke, M. M. Svenning, and T. Urich, “Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms,” ISME J. 7, 299–311 (2013).

    Article  Google Scholar 

  59. Z. Urbanová and J. Bárta, “Effects of long-term drainage on microbial community composition vary between peatland types,” Soil Biol. Biochem. 92, 16–26 (2016). https://doi.org/10.1016/j.soilbio.2015.09.017

    Article  Google Scholar 

  60. P. Vazquez, G. Holguin, M.E. Puente, A. Lopez-Cortes, and Y. Bashan, “Phosphate-solubilizing microorganisms associated with the rhizosphere of mangroves in a semiarid coastal lagoon,” Biol. Fertil. Soils 30, 460–468 (2000). https://doi.org/10.1007/s003740050024

    Article  Google Scholar 

  61. I. Verbaendert, N. Boon, P. De Vos, and K. Heylen, “Denitrification is a common feature among members of the genus Bacillus,” Syst. Appl. Microbiol. 34, 385–391 (2011). https://doi.org/10.1016/j.syapm.2011.02.003

    Article  Google Scholar 

  62. D. H. Wall, U. N. Nielsen, and J. Six, “Soil biodiversity and human health,” Nature 528, 69 (2015). https://doi.org/10.1038/nature15744

    Article  Google Scholar 

  63. K. D. Wendlandt, U. Stottmeister, J. Helm, B. Soltmann, M. Jechorek, and M. Beck, “The potential of methane-oxidizing bacteria for applications in environmental biotechnology,” Eng. Life Sci. 10, 87–102 (2010). https://doi.org/10.1002/elsc.200900093

    Article  Google Scholar 

  64. C. Winsborough, and N. Basiliko, “Fungal and bacterial activity in northern peatlands,” Geomicrobiol. J. 27, 315–320 (2010). https://doi.org/10.1080/01490450903424432

    Article  Google Scholar 

  65. Q. Zhong, H. Chen, L. Liu, Y. He, D. Zhu, L. Jiang, W. Zhan, and J. Hu, “Water table drawdown shapes the depth-dependent variations in prokaryotic diversity and structure in Zoige peatlands,” FEMS Microbiol. Ecol. 93, fix049 (2017). https://doi.org/10.1093/femsec/fix049

    Article  Google Scholar 

Download references

ACKNOWLEDGMENTS

This study was supported by the Malaysian Palm Oil Board (MPOB) Research Fund (Project no.: R009711000).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to N. A. Kusai.

Ethics declarations

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kusai, N.A., Ayob, Z. Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation. Eurasian Soil Sc. 53, 485–493 (2020). https://doi.org/10.1134/S1064229320040080

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1064229320040080

Keywords:

Navigation