Microbioma: La produzione primaria Marco Gobbetti...

Microbioma: La produzione primaria

Marco [email protected]

Sala Monumentale Presidenza del Consiglio, Roma, Italy 12th June 2019

Faculty of Science and Technology, Free University of Bolzano, Italy

mailto:[email protected]

Soil and sediments Crop primary production

Livestock primary production Marine primary productions

The CNNBSV standpoint – primary production


(CNBBSV 2019)

Increased productivity

Sustainable production

Waste recovery and by-products exploitation

Climate changes

Demographic development

How the system management has to improve/change?

Main challenges in crop production


(Mitter et al. 2016. Microb. Biotechnol. 9:635)

Soil microbiome

(Fierer, 2017. Nature Microbiol. doi:10.1038/nrmicro.2017.87)


Soil often contains >1,000 kg ofmicrobial biomass carbon per hectare

Distinct soil environments are onlymicrometres to millimetres apart

Soil is not a single environment, itencompasses a broad range ofdifferent microbial habitats

Climate, organisms, relief, parentmaterial and time

Soil properties (e.g., pH, organiccarbon, salinity, texture and availablenitrogen)

Soil microbiome with crucial roles innutrient cycling, fertility and carbonsequestration

O horizon

A horizon

B horizon

C horizon

Global microbial biomass found in soil



Soil biogeochemical processes modulated by microbiome



Solublephosphorus

Insolublephosphorus

H2O, OH-H+

Recalcitrantorganiccarbon

Labile organiccarbon

InorganicNitrogen

Organicnitrogen

S, Fe2+

Mn+2

NH4+

SO42- Fe3+

Mn+4 NO3-

N2 fixation, fermentation and methanogenesis

H2 oxidation

Methanogenesis

CH4+ oxidation

Respiration and fermentation

Carbon fixation

VOC production

VOC consumption

Denitrification and nitrification

N2 fixation and

NO/ N2O oxidation

Non-methane VOCsReduced nitrogen

(N2O, NO2, N2)

Plant as an holobiont, a meta-organism

HAIR

ORAL/SALIVARY

COLON

GUT

SKIN

VAGINA

OCULAR NASOPHARYNGEAL

LUNG

(Orozco-Mosqueda et al., 2018. Microbiol. Res. 1016:25)


vSTEM

LEAVESFRUITS

Above-ground plant microbiome

Below-ground plant microbiome

ROOTS

SEEDS

Epiphytes

Endophytes

Plants evolved with a pletora of bacteria,

fungi, archaea, protozoa and virus.

Testamentary mycorrhizal fungi date

back 700 million years ago

Arabidopsis thaliana, and Hordeum

vulgare, Zea mays, Oryza sativa, Glycine

max and Triticum aestivum

The plant bacterial microbiome is

dominated by Proteobacteria,

Actinobacteria, and Bacteroidetes

Diverse and well-balanced microbiome at

the plant–soil interface is vital in crop

production

The plant holobiont:


(Hassani et al. 2018. Microbiome 6:58)

vFRUITS

Above-ground plant microbiome

Below-ground plant microbiome

ROOTS

SEEDS

Epiphytes

EndophytesLEAVES

STEM

Surrounding environment: soil (main

reservoir) and air (minute

contribution)

Bulk soil (not influenced by the

plant root), rhizosphere (soil

influenced by the root), rhizoplane

and the endosphere (microbiota

inside the root)

Part of it could also be inherited

from the seed

Plants fine-tune their microbiomes

Where does the plant microbiome come from?


(Sanchez-Canizares et al. 2017. Current Opinion Microbiol. 38:188)

Plant domestication

(Pérez-Jaramillo et al., 2018. Microbiome 6:143)


Hordeum vulgare ssp. spontaneum vsHordeum vulgare ssp. vulgare

Firmicutes

BacteroidetesFlavobacteriaceae

Flavobacterium Flavobacterium

Flavobacterium

Staphylococcaceae

Oxolobacteraceae

Hyphomicrobiaceae

SphingomonadaceaeProteobacteria

Comamanadaceae

Biotic and abiotic drivers affecting the plant microbiome

Root exudates (e.g., organic acids,amino acids, phenolics, plantgrowth regulators … rizosphereeffect)

Soil type and factors (e.g., pH,salinity, structure, moisture,organic matter)

Environmnetal factors (e.g.,climate, agricultural practices,pathogen presence)

Plant compartments and species(e.g., genetics, host innate immunesystem, age, development stage,fitness, signaling)

(Compant et al., 2019. J. Adv. Res. 8:51)


Microbial and molecular interactions at the plantmicrobiome level


(Jansson and Hofmockel, 2018. Current Opinion Microbiol. 43:162)

Core plant microbiome: tightly associated with a certain plant genotype

Satellite plant microbiome: occurring in low abundance or in a reducednumber of sites

Meta-community: collection of populations connected by genetics,metabolic networking and organismal flow (holobiont – super-organism)

Plant growth (e.g., phytohormones - auxin, cytokinin and and gibberellin)

Cycling nutrient (e.g., phosphate and iron solubilisation, and nitrogen fixation)

Promotion of the establishment of mycorrhizal associations

Increased nutrient uptake and stress tolerance (e.g., indole and acetic acid)

Adaptive advantage and biocontrol activities (e.g., lytic enzymes, pathogen-

inhibiting volatile compounds and siderophores)

Modulating plant hormones level, and priming plant immune system and

systemic resistance

Decrease of the level of stress hormone ethylene (e.g., 1-aminocyclopro

pane-1-carboxylate –ACC- deaminase)

Sustainability (reduced chemical inputs, reduce emissions of greenhouse gases)

Driving food processing

Functions of plant microbiome



Faculty of Science and Technology, Libera Università di Bolzano, Italy

Fermented foods

Fermented Foods Are Up 149% - As

Long As They're Unfamiliar

Forbes, Feb 6, 2019

Fermented foods are one of the top 10 food trends in 2016

(Riley, 2015), continuing the trend over the last few years.

Traditional Novel

Art. 5. (Prodotti utilizzabili per la lievitazione nella panificazione) – punto5: È definito «pasta madre» o «lievito naturale» l’impasto ottenuto confarina e acqua, sottoposto a una lunga fermentazione naturale acidificanteutilizzando la tecnica dei rinfreschi successivi al fine di consentire lalievitazione dell’impasto. La fermentazione deve avvenire esclusivamente aopera di microrganismi endogeni della farina o di origine ambientale. …

The sourdough definition (pasta madre, lievito madre,impasto acido)


The sourdough preparation

0 1 2 5 10 0 1 2 5 10 0 1 2 5 10 days of refreshments

Rye Triticum durum T. aestivum

Microbial dynamics during sourdough preparation(Ercolini et al., 2013. Appl. Environ. Microbiol., 79:7827)

(days of refreshments)

T. durum


The house microbiota

L. sanfranciscensis in sourdough

L. sanfranciscensis in sourdough (year 2006)L. sanfranciscensis in bakery air (year 2008)

L. plantarum in sourdoughL. plantarum in flourL. plantarum on baker’s hand (year 2008)L. plantarum in sourdough (year 2007)

(Scheirlinck et al., 2009. J Appl Microbiol, 106:1081-1092)

99,992121,3272,1255 5,9081655,9081655,908165O

S

F

F

FDM

SB

WB

20,88620,886 20,88642,395399,9921

0,05SB

S DM

F F FWB

O

0,3653780,3653780,36537810,8883842,3953 0,3653780,365378 0,3653780,05

WB

DM

SO

FF

F

F

F

F

SB

4,1679914,1679914,167991 99,9921

75,2465859,56605

O F FF SB

SWB

DM

AM.B MT.A MT.D VZ

0100

SB, storage box; DM, dough mixer; F, flour; S, sourdough

(Minervini et al., 2015. Food Microbiol. 52:66-76)

L. sanfranciscensis


Ingredients and tap water (Minervini et al., 2016. Food Microbiol. 60:112; Minervini et al., 2019. Sci. Reports 9:250)

Lactic acid bacteria species diversity


Table 3. Species and strains of lactic acid bacteria isolated from mature sourdoughs prepared using 10 different tap waters, at the end of the last

fermentation. The dot indicates the presence of strains.

Abruzzo Basilicata Campania Lazio Lombardia Puglia Toscana Trentino-Alto

Adige

Umbria Veneto

Lactobacillus curvatus s1 ● ● ● ● ● ●

Lactobacillus plantarum s4 ● ● ●

L. plantarum s5 ● ● ● ●

L. plantarum s6 ● ● ●

L. plantarum s7 ●


L. plantarum s9 ● ●



L. plantarum s12 ●




Leuconostoc citreum s1 ●

Ingredients

Tap water

Tap water

Chemicalcomposition

Flour harbors lactic acid bacteria

(Alfonzo et al., 2013. Food Microbiol, 36:343-354; Coda et al., 2010. J Appl Microbiol, 108:925-935)


Lactic acid bacteria as endophyte components of thedurum wheat plant (Minervini et al., 2015. Appl. Environ. Microbiol. 81:6736)


Durum wheat dough singlyinoculated with Lactobacillus

sanfranciscensis A4 and…

Nine doughs (includingthe control, with no

microbial inoculation)

PropagationWheat endophytic strains:1. Lactobacillus plantarum LA12. L. plantarum LB23. L. plantarum OLB34. L. plantarum OLD15. L. plantarum OLB46. L. plantarum OLC47. Lactobacillus rossiae OLC18. Enterococcus faecalis LA2 De novo sourdoughs

Parallel propagation (one week) at artisan bakery and laboratory level L. plantarum LB2 dominated all the sourdoughs under all the different conditions of propagation

LB

2.A

1

LB

2.A

2

LB

2.A

3

LB

2.A

4

LB

2.A

5

LB

2.A

6

LB

2.A

7

LB

2.A

8

LB

2.A

9

LB

2.A

1

0 LB

2.A

1

1 LB

2.A

1

2 LB

2.A

1

3 LB

2.A

1

4 LB

2.A

1

5 LB

2

LB

2.A

1

6 LB

2.A

1

7 LB

2.A

1

8 LB

2.A

1

9 LB

2.A

2

0 LB

2.A

2

1 LB

2.A

2

2 LB

2.A

2

3 LB

2.A

2

4 LB

2.A

2

5 LB

2.A

2

6 LB

2.A

2

7 LB

2.A

2

8 LB

2.A

2

9 LB

2.A

3

0 LB

2.A

3

1


Robustness of endophyte components

(Minervini et al., 2018. Food Microbiol. 70:162)

From wheat plant to sourdough: the microbiome fil rouge

(Gobbetti et al., 2019. Crit. Reviews Food Sci Nutr. In press)


0,3653780,3653780,36537810,8883842,3953 0,3653780,3653780,3653780,05

WB

DM

SO

FF

F

F

F

F

SB

MT.DHouse microbiota

Technological process parameters

Agricultural parameters

Ingredients and Tap water

(De Vuyst et al., 2014; Minervini et al., 2012; Kashiuvagi et al., 2009; Vancanneyt et al., 2005; Meroth et al., 2003)

L. acetotolerance, L. acidifarinae, L. acidophilus

L. alimentarius, L. amylovorus , L. amylolyticus

L. arizonensis, L. brevis , L. buchneri, L. casei,

L. cellobiosus

L. collinoides, L. crispatus,

L. crustorum, L. curvatus

L. delbrueckii, L. farciminis,

L. fermentum

L. fructivorans, L. frumenti,

L. gasseri, L. gallinarum,

L. graminis, L. guizhovensis

L. hammesii, L. helveticus, L. hilgardi,

L. homoiochii, L. kimchi, L. kunkeei

L. johnsonii, L. mindensis

L. mucosae, L. nagelii, L. namurensis

L. coryniformis, L. colehominis,

L. nantensis, L. nodensis, L. oris

L. parabrevis, L. parabuchneri,

L. paracasei, L. paralimentarius,

L. pentosus, L. perolens

L. plantarum, L. pontis, L. reuteri

L. rhamnosus, L. rossiae,

L. saivarius, L. sakei,

L. sanfranciscensis,

L. siliginis, L. secaliphilus,

L. spicheri , L. panis

L. vaginalis, L. zaea,

L. zymae

The sourdough microbiome is extremely diverse


The first sourdough “microbiome library" (Saint-Vith, Belgium) in the world


Modulation of plant microbiota



Inoculation of single strain

Application of microbial

consortia

Plant selection

Mode of delivery

Microbiome engineering

Meta-community approach

Microbiome research from fundamental to applied –

Needs and Directions

Multi - omics Microbe isolation and phenotyping

Ap

pli

ed

Fu

nd

am

en

tal

- Combined use of omics

coupled with analytical

methods

- Use of alternative microbial

gene/taxonomic markers

- Need for comprehensive

databases

- Use of standardised

methods

- Genomic / functional characterization of

isolates

- Testing of isolates for novel PGP traits

- Validation of binary microbial

interactions

- Application of synthetic communities

- Investigating the rare microbiome,

microbes with altered lifestyle and

understudied taxa

- Effect of soil characteristics/farming

practice on microbiome

- Disease suppression in soil

- Potential of seed microbiome

- Microbiome engineering

Microbiomics in agriculture

Micro4food Lab: running EU projects


1. FUNBREW - Biotransformation of brewers´ spent grain:

increased functionality for novel food applications (European Union

ERANET/SUSFOOD)

2. SMART Protein - Alternative proteins for food and feed

(Horizon 2020, LC-SFS-17-2019)

3. Knowledge Platform on Food, Diet, Intestinal Microbiomics and

Human Health (JPI, ERA-HDHL INTIMIC)

4. Knowledge Hub on Food and Nutrition Security (JPI, ERA-

HDHL)

Microbioma: La produzione primaria Marco Gobbetti...

Documents

Transcript of Microbioma: La produzione primaria Marco Gobbetti...