Environmental Engineering Reference
In-Depth Information
1.
I
NTRODUCTION
Wetlands, make up an estimated 45% of the total value of global natural ecosystems [1],
are one of most important terrestrial ecosystems and distribute in all regions of throughout the
world including Antarctica [2]. Microbiomes in wetlands play an important role in
biogeochemical processes and microbial activities are crucial to the functions of wetland
systems [3-8]. Moreover, its diversity is essential for exploiting potential of microbial
resources from the wetland ecosystems [9-13]. It is crucial and necessary to understand the
overall survival microorganisms in wetlands. Bacteria and archaea have been widely studied
with respect to their biodiversity in natural and constructed wetlands [14-17]. Initial studies
employed traditional culture-dependent methods and resulted in the discovery of plenty of
new bacterial and archaeal taxa [18]. Employing kinds of molecular biology methods,
increasing evidences have suggested that the structures of microbial communities are related
to soil processes, such as cloning and sequencing of 16S rRNA genes, denaturing gradient gel
electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and
quantitative PCR [4, 8, 19-23]. Cloning and sequencing of 16S rRNA genes have been widely
used for its identification of potential known and unknown microbes [24]. Plenty of studies
have examined the microbial diversity in wetlands using relatively large (>200 sequences)
16S rRNA clone libraries [4, 20, 25]. However, most studies to date have focused on
individual wetland ecosystems [16, 26-28]. Many of the datasets published contain a small
number of cloned sequences (generally >100), thus revealing only a small portion of the full
diversity present in wetlands [10, 11, 29, 30]. The focus of some studies is limited on
particular microbial group [31, 32]. In addition, there are many sequences recovered from
wetlands with no additional information which were deposited into GenBank without being
reported yet. High-throughput sequencing technologies, such as 454-pyrosequencing and ion
torrent, were used to analyze the microbiomes in wetlands [30, 33-35]. These methods can
produce huge datasets of short sequence reads. However, the length of these reads is too short
to classify. Currently, there is no consensus on the size or nature of the microbial diversity
generally found in wetlands. As a result, the understanding of the microbiomes in wetlands is
fragmented and likely biased. This knowledge gap of microbiomes in wetlands will hamper
the efficiency and stability of wetlands ecosystems. Few of the collective overview of the
microbial diversity in global wetlands is found up to date. The purposes of the study are to (1)
perform a meta-analysis of all publicly available 16S rRNA gene sequences identified from
various wetlands to provide a collective appraisal of the microbial diversity in wetland
ecosystem, (2) make an effort to estimate the current coverage of the microbial diversity in
wetlands and (3) identify particular gaps in the knowledge and understanding of the microbial
populations involved in wetlands.
2.
M
ETHODS
2.1. Sequence Data Collection
Initial sequence sets were obtained from the GenBank (http://www.ncbi.nlm.nih.gov) and
RDP (Release 10, http://rdp.cme.msu.edu) databases using the search terms ('wetland' OR
