Botanical Studies (2009) 50: 57-68.
*
Corresponding author: E-mail: ssyang@ntu.edu.tw; Te l:
+886-2-33664456; Fax: +886-2-23679827.
INTRODUCTION
Soil microbes are essential components of the biotic
community in natural forests and are largely responsible
for ecosystem functioning (Hackl et al., 2004). The
microbial composition of the soil surface horizon has been
far better studied than that of the deeper horizons (Agnelli
et al., 2004). Microbes in the deeper horizons also play an
important role in ecosystem biogeochemistry (Madsen,
1995). It is not clear whether the subsurface microbial
community is closely related to the surface microbial
community or is an independent ecosystem with a distinct
assemblage of microorganisms (Fierer et al., 2003).
About 1% of the total number of microbes present in
soil is culturable (Schoenborn et al., 2004), hindering
analysis of microbial diversity using culture-based
methods. Various biochemical and molecular techniques
have been used to more completely and precisely
characterize microbes from the natural environment (Liu et
al., 2006). Although every method has its advantages and
limitations, 16S rRNA gene-based molecular techniques
have commonly been used to analyze the phylogenetic
diversity of bacterial communities (Chow et al., 2002).
Polymerase chain reaction (PCR) amplification of 16S
rDNA followed by separation of the PCR products on
a denaturing gradient gel electrophoresis (DGGE) is an
important method for analysis of bacterial communities
(Muyzer et al., 1993). Bacterial species can be identified
by generation of 16S rDNA clone libraries followed
by sequencing and comparison with databases of
ribosomal sequences, enabling phylogenetic affiliation to
cultured and uncultured microorganisms (Maidak et al.,
1999). These techniques have proven very suitable for
comparative fingerprinting of soil samples (Watanabe et
al., 2004).
A number of studies have shown that even small-
scale topographical landforms can alter environmental
conditions, which in turn retard or accelerate the activity
of organisms (Scowcroft et al., 2000). The effects
of topographical landforms on species composition,
productivity, environmental conditions, and soil
characteristics have been well investigated (Barnes et al.,
1998), but very few studies have investigated the effects
of these different environmental conditions on microbial
diversity.
The Fushan forest is one of the four natural forest sites
in the Taiwan Long Term Ecological Research Network
(TERN) to study the effect of environmental disturbances
such as typhoon and acidic deposition on ecosystem
function (Lin et al., 2000; Lin et al., 2003b; King et al.,
2003; Liu et al., 2004). However, a few studies have been
Soil bacterial community composition across different
topographic sites characterized by 16S rRNA gene
clones in the Fushan Forest of Taiwan
Shu-Hsien TSAI
1
, Ammaiyappan SELVAM
1
, Yu-Ping CHANG
1
, and Shang-Shyng YANG
1,2,
*
1
Institute of Microbiology and Biochemistry, and
2
Department of Biochemical Science and Technology, National Taiwan
University, Taipei 10617, Taiwan
(Received February 5, 2008; Accepted August 15, 2008)
ABSTRACT.
Bacterial communities present in soils from the valley, middle-slope, and ridge sites of the
Fushan forest in Taiwan were characterized using 16S rDNA analysis of genomic DNA after polymerase
chain reaction amplification, cloning, and denaturing gradient gel electrophoresis analysis. Phylogenetic
analysis revealed that the clones from nine clone libraries included members of the phyla Proteobacteria,
Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae,
Planctomycetes, candidate division TM7, and Verrucomicrobia. Members of Proteobacteria, Acidobacteria, and
Actinobacteria constituted 49.1%, 32.3%, and 6.3% of the clone libraries, respectively, while the remaining
bacterial divisions each comprised less than 6%. The ridge site exhibited the most bacterial species number,
indicating the influence of topography. Bacterial composition was more diverse in the organic layer than in the
deeper horizons. In addition, bacterial species numbers varied across the gradient horizons.
Keywords: 16S rDNA library; Acidobacteria; Bacterial community; DGGE; Proteobacteria; Topography.
mICROBIOlOgy