Soil as a Support of Biodiversity and Functions - Soil Carbon: Science, Management and Policy for Multiple Benefits - page 145

together with their highly significant reduc-
tion in cost (the price of high-throughput se-
quencing has fallen from US$5292 down to
US$0.09 per DNA megabase over the past dec-
ade; http://www.genome.gov/sequencingcosts/)
corresponds to a major technical revolution
for the characterization of the diversity of
soil microbial communities. More precisely,
pyrosequencing allows several tens of thou-
sands, even hundreds of thousands, of DNA
sequences to be obtained from a single meta-
genomic DNA. It represents, consequently,
the most powerful method to date to quan-
tify precisely and characterize microbial
diversity through the identification, in a
holistic way, of the microbial populations
in complex environments (Roesch et al ., 2007;
Fulthorpe et al ., 2008). Two complementary
strategies can be distinguished for these
metagenomics approaches. The first strategy
consists of analysing all the DNA sequences
extracted from the indigenous communities
in a given environment by targeting either a
gene providing particular taxonomic infor-
mation (ribosomal genes) (Terrat et al ., 2012)
or functional data (functional genes) (Philippot
et al ., 2013). The second strategy is based on
the mass sequencing of all DNA fragments
without targeting specific genes (sequen-
cing of all the metagenome). This approach
is highly promising and has proved particu-
larly useful in analysing metagenomes from
the Sargasso Sea (Dalton, 2004), an acid
mine (Tyson et al ., 2004), the digestive tube
(Qin et al ., 2010) and a soil (Vogel et al ., 2009).
However, it is time- and cost-consuming
and still requires important bioinformatics
developments, which limits the number of
samples that can be analysed and conse-
quently the application of this strategy for
ecological studies. In contrast, the first strat-
egy allows a very large number of environ-
mental situations to be examined, and thus
appreciation of a variety of environments.
In addition, by the targeting of a limited
number of genes, it provides access to the
taxonomic and functional diversities of
communities involved in particular ecosys-
temic services. Roesch et al . (2007) used
this strategy to characterize microbial di-
versity in four soils originating from distant
geographical locations (USA, Canada and

Brazil). Such studies represent the first ex-
haustive descriptions of the enormous rich-
ness of soil bacterial diversity. Fulthorpe et al .
(2008) then produced an alternative ana-
lysis of these data, and demonstrated the
weak similarity in community composition
between the soils, thereby revealing that
distantly sampled soils carried few species
in common. These data support the hypoth-
esis that various pedoclimatic characteris-
tics, as well as land-use and soil management
history, can lead to different indigenous
microbial diversities. Pyrosequencing tech-
niques were also used in other investiga-
tions to decipher soil microbial diversity
and elucidate the distribution of diversity
within particular taxonomic groups of soil
bacteria. Jones et al . (2009) sampled and
characterized soils from North to South
America (from Alaska to Patagonia) to de-
termine the influence of abiotic soil param-
eters on the abundance of Acidobacteria.
They used this approach to define the eco-
logical attributes of the targeted groups and
to rank the environmental parameters that
most explained their spatial distribution.
Limited knowledge of the taxonomic and
functional sequences is one of the main
blocks restricting our ability to identify new
species or new functional genes. Although
few studies have been published as yet, the
scientific community is unanimous in affirm-
ing the relevance and enormous potential
of this type of approach for characterizing
the diversity of soil microorganisms (Christen,
2008). Application of the methods described
in this section on suitable samplings brings
precious knowledge for our understanding
of the importance of SOM as a driver of the
microbial abundance and diversity in soil.

Organic Matter as a Support of Soil
Biodiversity

Soil represents a highly complex and het-
erogeneous matrix. This property has strong
repercussions on the distribution of both
nutritive resources (Arrouays et al ., 2001)
and organisms in soil. Indeed, at the micro-
scale, soil provides a heterogeneous habitat