Agriculture Reference
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pyrosequencing (also known as massive sequencing) and single-molecule sequencing
have the potential to make these projects considerably more cost efficient and productive.
The science of metagenomics involves genome-level characterization of whole micro-
bial communities on a culture-independent and high-throughput scale. While sequencing
answers questions about evolutionary relationship (phylogenetics), metagenomics has the
potential to determine how communities are functioning in a given environment (Singh
et al., 2004).
A promising metagenomics approach is the construction of bacterial artificial chromo-
some (BAC) clone libraries to define communities based on particular functional genes
that are present and potentially active in the community. Screening of BAC libraries for
functional genes has identified both novel and previously recognized antibiotics (Rondon
et al., 2000), antibiotic resistance genes (Diaz-Torres et al., 2003), enzymes (Henne et al.,
2000), and a protein involved in a novel photosynthetic pathway that may play a significant
role in the global carbon cycle in the sea (Beja et al., 2000). Current BAC methods rely on
the use of an
Escherichia coli
gene expression vector, but advancement of this approach will
require the development of additional expression vectors because only a limited number
of genes can be expressed in
E. coli
.
Gene arrays using reverse transcribed messenger RNA (mRNA) and designed for a
community of interest can assess information about gene diversity and expression. These
techniques are still in their infancy, particularly when applied to natural communities. As
the database of environmental functional genes grows, habitat-specific microarrays will
provide quantitative information about community gene expression. In addition to more
database information, enhancement of array technology for greater sensitivity and speci-
ficity requires improved methods for extraction of nucleic acids from soil and improve-
ment in data analysis tools.
2.1.2.2 Mitigating factors for the power of metagenomics
The high species diversity of soils and rhizospheres seemingly has led to functional redun-
dancy, which would suggest functional characteristics of component species are at least as
important or perhaps more important than species diversity per se for maintaining essen-
tial processes (Andrén and Balandreau, 1999; Bardgett and Shine, 1999). Undoubtedly,
some minimum but likely large number of species living in stable communities is essential
for mediating biogeochemical processes to enable ecosystem function in changing envi-
ronments, the so-called insurance hypothesis (Loreau et al., 2001).
Unlike higher life-forms for which species can be clearly defined, the avalanche of
genomic data indicates that defining species diversity or even the concept of species for
microorganisms is becoming increasingly difficult. In part this is due to the growing rec-
ognition of
horizontal gene flow
(HGF) (nongenealogical transfer of genetic material from
one organism to another) among bacteria or between viruses and bacteria. HGF has impli-
cations for defining how many species there actually are in soils and suggests that, rather
than discrete genomes, there are genetic continuums (Golenfeld and Woese, 2007). In this
scenario, microorganisms absorb or abandon genes as needed to adapt to environmental
conditions. Furthermore, this would suggest that microorganisms are largely cooperative
in terms of survival and function.
Complicating our understanding of species diversity, the role of gene transfer in
the environment is a largely unknown entity. It is important to develop experimen-
tal tools that can precisely determine the mechanisms and location of gene transfer in
soils and rhizospheres to exploit microbial-plant interactions to fully utilize the power
of genomics. In addition, it will be important not only to identify putative beneficial
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