This presentation was presented during Day 3 of the Global Soil Partnership Plenary Assembly – 5th Session that took place at FAO Hq in Rome, Italy, from 20 to 22 June 2017. The presentation was made by Ms. Annamaria Bevinino

2. Annamaria Bevivino | ENEA
Italian National Agency for New Technologies, Energy
and Sustainable Economic Development
annamaria.bevivino@enea.it

3. Why is soil biodiversity so
important in keeping soil
healthy? A case study in the
Mediterranean area
- funghi: Acremonium zeae, Ampelomyces quisqualis, altre zone della stessa unità di coltivazio
che è nata l’idea di prelevare campioni di
sivi da distribuire nelle aree colpite. Tutta
sività in questi casi si riesce a indurre p
mediante l’apporto di matrici organiche
compost, ecc. (Pugliese et al., 2006). Lo
ste manifestazioni ha portato all’isolamen
di microrganismi utili, in partico
(Agrobacterium spp., Bacillus spp., Burk
Xanthomonas maltophilia, Serratia
Pseudomonas fluorescens, P. paucimobil
ciens, P. pyrrocinia, P. acidula, P. a
mephitica, P. ovalis, ecc.) e funghi anta
comuni nei terreni (Trichoderma, Gliocla
Sono state identificate inoltre specie di fu
parassiti (Beauveria bassiana, Metarh
Foto 2 – Alcuni miliardi di anni fa i batteri iniziarono il processo di
colonizzazione del nostro pianeta, differenziandosi in numerosissime
specie che a tutt’oggi molte sono ancora sconosciute. Questi micror-
ganismi oltre che a vivere in simbiosi con uomini e animali (in parti-
colare nel tratto dell’apparato digestivo) determinano la fertilità dei
terreni (microflora batterica).

4. • Soil contamination is a worldwide problem
with serious associated environmental
impacts and health risks
• The widespread contamination of soils with
various pollutants creates toxicological risks
associated with their use in agriculture,
groundwater contamination and therefore
food, social and health security
• The need for “clean” soils is a prerequisite
for safe agricultural production
SOIL CONTAMINATION: BACKGROUND

5. THE ROLE OF SOIL MICROORGANISMS
Microorganisms
• Represent the most important and diverse group of organisms
• Play a central role in ecosystems functioning
• Soil bacteria play a central role in decomposing organic matter, in
determining the release of mineral nutrients, and in nutrient
cycling
Modified from Johannes Sikorski SOIL ORGANISMS 2015

6. A schematic of how disturbance can
change microbial composition and
thereby affect ecosystem processes
versus when disturbance would not
have this effect (when the microbial
community is resistant, resilient or
functional redundant)
Steven D. Allison, and
Jennifer B. H. Martiny
PNAS 2008;105:11512-
11519
HOW DISTURBANCE CAN AFFECT MICROBIAL COMMUNITY
COMPOSITION

7. SOIL CONTAMINATION AFFECTS SOIL
MICROBIAL DIVERSITY
Microorganisms in contaminated soil are
disrupted, leading to a decline in soil
biodiversity, aggregate stability and
decomposition processes
http://www.recare-hub.eu/soil-threats/contamination

8. How to measure belowground biodiversity?
Does it matter if one species disappears? Can
other species replace its function?
MICROBIAL DIVERSITY: OPEN QUESTIONS
May microorganisms be used as
bioindicators in soil?

9. EFFECT OF SOIL CONTAMINATION ON SOIL
MICROORGANISMS
 Survival
 Population structure
 Community/ecosystem
Mark Hodson, Soil pollution and its impact on soil life 29
Effect on soil organisms
• Metabolic cost
• Survival
• Population structure
• Community / ecosystem

10. METHODS OF STUDY OF MICROORGANISMS
Sample
Biochemical-
microbiological
methods
Plate-count method
Community-level
physiological
profiling) (Biolog)
FAME Analysis
Molecular
methods
GC content
Microarray
DGGE
TGGE
RFLP
T-RFLP
DNA sequence
analysis
Genomics
Metagenomics
L. JENNIFER et al.(2004) Methods of studying soil microbial
diversity. Journal of Microbiological Methods

11. Only 1-10% of all soil
bacteria are considered
to be culturable
Vogel et al. 2009 Nature Reviews Microbiology 7, 252
CULTURE-BASED METHODS
• species may be uncultivable
• some species require special conditions
• species in relatively low density

12. • Access to a much larger reservoir of
genomic and metabolic information
• Link community structure and diversity
to function
CULTURE-INDEPENDENT METHODS

13. Genomics Metagenomics
J.C.WOOLEY et al.(2009);«Extending Standards for Genomics and Metagenomics Data…»;
Standard in Genomic Science
Link between
them

14. QUANTIFYING THE EFFECTS: A META’OMICS APPROACH
Soil microbiome Soil sampling DNA extraction

15. Microbial community complexity
Complex microbiota
N° species
(Richness)
Abundance
(Evenness)
Richness
Evenness
Richness
Evenness
High
complexity
Low
complexity

16. A CASE STUDY: BERCHIDDA (SARDINIA, ITALY)
PA
TV
CV
CO
MM
PROFILES:
GRASS COVERED VINEYARD (CV)
TILLED VINEYARD (TV)
CORK-OAK FOREST (CO)
MANAGED MEADOW (MM)
PASTURE (PA)
The Mediterranean area is one of the most important biodiversity hotspots in the world

17. Increase of anthropic impact
LONG-TERM EFFECTS OF DIFFERENT LAND-USE WITH INCREASING
LEVEL OF INTENSIFICATION IN SPRING AND AUTUMN

18. EXPERIMENTAL PROCEDURE
CORK-OAK FOREST (CO)
MANAGED MEADOW (MM)
PASTURE (PA)
COVERED VINEYARD (CV)
TILLED VINEYARD (TV)
I, II, III, IV, V
I, II, III, IV, V
I, II, III, IV, V
I, II, III, IV, V
I, II, III, IV, V
Culture-based analysis
Molecular analysis
Soil physical-
chemical-biological
characterization

19. Cluster analysis of molecular data
• Cluster analysis revealed a separation between
communities recovered in autumn and in spring
• Within each season, the presence of bacterial
communities subgroups associated to different
land uses was observed

20. Culture-based analysis

21. Conclusions
• Soil bacterial communities exhibited compositional shifts that tracked
with changes in land use and soil management
• Soils subjected to low human inputs showed a more stable bacterial
community than those with high human input
• Our study combining the pedological and biochemical data with
microbiological and molecular analysis furnish a good methodological
approach to describe the influence of different soil managements on
the soil microbial community structure
PLoS ONE 2014, 9(8): e105515.

22. SOIL: the gleyic fluvisol coming from the alluvium of the Litavka
river (Láz close to Příbram City, Czech Republic), containing a
negligible amount of nutrients (9% SOM) and Pb and Zn for a
total content up to 100 ppm.
Biochar impact on microbial community structure and plant
growth in soil with low-level of metal contamination
Arianna Latini (ENEA), Annamaria Bevivino (ENEA), Alessio Mengoni (University of Florence), Manuel
Teodoro (University of Life Science Prague), Lukas Trakal (University of Life Science Prague)

Boruvka L., Vacha R. (2006) Litavka river alluvium as a model area heavily polluted with potentially risk
elements. In: Morel JL., Echevarria G., Goncharova N. (eds) Phytoremediation of Metal-Contaminated Soils.
NATO Science Series, vol 68. Springer, Dordrecht

23. Linking belowground biodiversity and ecosystem function in
European forests (BioLink)
FPS COST Action FP1305
www.bio-link.eu
Chair of the Action:
Dr Martin Lukac (UK)
STSM call - Early Stage Researchers
Deadline 15th July 2017 http://www.bio-link.eu/stsms/

24. Contacts:
annamaria.bevivino@enea.it
Phone +39 06 30483868
Skype: a.bevivino
THANK YOU FOR YOUR ATTENTION