Agriculture Reference
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aiming at linking soil biodiversity with
ecosystem services, with a specific focus on
C cycle.
the biomass obtained after fumigation extrac-
tion, is that it can be measured on dry soil
samples, which means that it can be deter-
mined at the same time as physico-chemical
analyses, using a moderate-throughput sys-
tem to establish reference values for inter-
preting the results.
Total community (bacteria or fungi),
functional communities, or those belonging
to a particular taxonomic group, can also be
quantified from soil DNA extracts by apply-
ing quantitative PCR to determine the num-
ber of copies of the rRNA genes (whole
communities), the functional gene shared
by populations in the functional commu-
nity or of a specific sequence in the targeted
taxonomic group, respectively. One example
of a functional group concerns bacteria with
the ability to reduce nitrous oxides (Regan
et al
., 2011). For example, Regan
et al
.
(2011), by quantifying denitrifying genes
(
nirK
,
nirS
,
nosZ
) in a permanent grassland
under elevated atmospheric CO
2
, showed
that high N
2
O emissions under elevated CO
2
correlated with lower nosZ to nirK ratios,
suggesting that increased N
2
O emissions
under elevated CO
2
might be caused by a higher
proportion of N
2
O-producing, rather than
N
2
O-consuming (N
2
-producing) denitrifiers.
From a qualitative point of view, com-
munities can be characterized either by their
structure, i.e. assemblage of the different
constitutive populations, or their diversity,
i.e. the different types of organisms present.
The genetic structure is classically deter-
mined by the molecular fingerprints of the
communities (for review, see Ranjard
et al
.,
2001). Until recently, comparisons between
studies were hampered by the great variety
of techniques employed, and an effort of stand-
ardization was clearly required. This has
been undertaken by national and European
programmes (Gardi
et al
., 2009), such as
those conducted in the UK (Countryside
Survey,
http://www.countrysidesurvey.org.uk
)
,
in France (Network for the Measurement of
Soil Quality, Réseau de Mesure de la Qual-
ité des Sols - RMQS,
http://www.gissol.fr/
programme/rmqs/rmqs.php
) and in Europe
(EcoFINDERS,
http://ecoinders.dmu.dk/
)
.
The recent progress achieved with new
high-throughput sequencing technologies
Methods of Characterization of Soil
Microbial Communities
The scientific domain described as 'micro-
bial ecology' is about
50
years old, and is
thus young. Its step-by-step evolution has
been promoted mainly by methodological
Among these developments, numerous mo-
lecular tools are now available to character-
ize the microbial information contained in
the nucleic acids extracted from environ-
mental samples (Swift
et al
., 1998; Qin
et al
.,
2010). They allow the routine characteriza-
tion of variations in microbial community
abundance, structure and diversity in mul-
tiple situations (for review, see Ranjard
et al
.,
2001). With the development of these so-
called 'molecular ecology' approaches, the
number of studies dedicated to the charac-
terization of microbial communities in vari-
ous environments or subjected to different
perturbations has increased exponentially
(Morris
et al
., 2002). All these studies are
highly promising and are providing insights
into chronic or punctual modifications of
microbial biodiversity in natural environ-
ments.
Total microbial communities and those
determining particular functions or belong-
ing to specific taxonomic groups of particular
interest or presenting a danger can therefore
be quantified. The abundance of total mi-
crobial communities can be measured from
the microbial molecular biomass (Dequiedt
et al
., 2011). The microbial biomass is a
well-known marker of soil biological func-
tioning (Horwath and Paul, 1994) and repre-
sents a sensitive and early indicator of changes
of soil management (farming practices, con-
tamination; Ranjard
et al
., 2006). It is deter-
mined by quantifying the microbial DNA in
soil extracts and is correlated with the mi-
crobial biomass (Marstorp
et al
., 2000; Leck-
ie
et al
., 2004) measured after fumigation
extraction (Vance
et al
., 1987). The advan-
tage of molecular biomass, compared with
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