Agriculture Reference
In-Depth Information
tomato Fusarium wilt disease. The carbon types distribution among several molecu-
lar classes incite changes in microbial structure, that can be evidenced by specific
metabolic profiles used to distinguish non-suppressive from suppressive situations
(Itoh et al.
2002
). For example, Borrero et al. (
2006
) reported that Biolog culturable
community, extracted from Fusarium wilt-suppressive compost, prefer not easily
biodegradable compounds, such as carboxylic acids, aminoacids, amines, phenolic
compounds and polymers, than non-suppressive ones. Similarly, Pane et al. (
2013
)
pointed out the relation between the ability of suppressive community to metabo-
lize complex carbon sources and the relative abundance of hydrophobic C in the
compost. The compost is a highly complex and dynamic environment that sustain
a great diversity of microbes that are involved directly and indirectly in the pro-
vision of a wide range of ecosystem services. The microbial structure more than
the size of diversity in the compost is believed, generally, directly related to dis-
ease suppressivity (Xu et al.
2012
). Thus, it is imperative to increase the level of
understanding of compost microbial ecology and population dynamics. Changes
in compost microbial community structures have been extensively explored with
holistic approach by using various tools ranging from traditional plate counting
and biochemical-based cultural methods until to innovative molecular-based tech-
niques and “omic” strategies, including metagenomic analysis. Newer researches to
measure compost microbial biodiversity, in fact, are focusing on genetic diversity
viewed as the amount and distribution of genomic information within the general-
ity of microbial living species. Metagenomic strategy analyze the set of the total
microbiota genomes, termed metagenome, extracted from indigenous community
in a given substrate (Rondon et al.
2000
). This approach have a lot of credit respect
to traditional methods that provide very limited information, because only a small
percentage of total soil microbiota, estimated between 0.1 and 10 %, is cultivable
In-vitro (Torsvik and Øvreås
2002
). Hadar (
2011
), reviewing on the role of com-
post microbial ecology in suppressivity, stressed the opportunities coming from the
application in this field of the next generation sequencing technologies including
metagenomics, metatranscriptomics and bioinformatics. Studies on microbiota di-
versity in suppressive composts by molecular approach are increasing in this de-
cade and concur to distinctly clarify implied groups. For example, Pérez-Piqueres
et al. (
2006
) described a clear influence of different types of compost on bacterial
and fungal communities composition in enhanced suppressive soils by using termi-
nal restriction length polymorphism (T-RFLP). While a PCR-DGGE methodology
has used to evidence the positive influence of compost amendment on rhizospheric
streptomycetes (Inbar et al.
2005
) and fungal (Kowalchuk et al.
2003
) commu-
nity composition. PCR amplified and cloned metagenomic sequences revealed that
compost inoculation of the pathogenic oomycetes
Pythium ultimum
induces dis-
tinct shifts in microbial community favouring α-Proteobacteria suppressive groups
(Hagn et al.
2008
). Obviously, differential changes in microbial structure can be
associated to modification of compost bioactivities. van Rijn et al. (
2007
) found
that only significant shifts in 16S-rDNA DGGE banding patterns of the composts,
occurred during storage, are related to significant reduction of suppression of
Fu-
sarium oxysporum
f. sp.
lini
.
