Applied Microbiology and Biotechnology

, Volume 100, Issue 4, pp 1999–2010 | Cite as

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem

  • Seung-Hoon Lee
  • Hojeong KangEmail author
Environmental biotechnology


The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 1011, 1.10(±0.06) × 1011, and 4.33(±0.16) × 1010 g−1 soil; nirS were 5.41(±1.25) × 108, 4.93(±0.94) × 108, and 2.61(±0.28) × 108 g−1 soil; and nirK were 9.67(±2.37) × 106, 3.42(±0.55) × 106, and 2.12(±0.19) × 106 g−1 soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.


Estuary Soil depth Invasive plant Bacteria Denitrifiers Microbial activity Community composition 



This study was supported by ERC (No. 2011-0030040).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

253_2015_7111_MOESM1_ESM.pdf (122 kb)
ESM 1 (PDF 121 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.School of Civil and Environmental EngineeringYonsei UniversitySeoulSouth Korea
  2. 2.Geobiotech CorporationSeoulSouth Korea

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