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The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover Institute of Soil Science 12.2.2009 Bodenkundliches Kolloqium Georg Guggenberger, Florian Carstens ([email protected]) KEYSOM 1 st Training School Coimbra, October 4-7, 2016

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Page 1: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

The interactions between soil biota,

soil structure, and SOM dynamics

Leibniz University Hannover ■ Institute of Soil Science

12.2.2009 Bodenkundliches Kolloqium

Georg Guggenberger, Florian Carstens([email protected])

KEYSOM – 1st Training School

Coimbra, October 4-7, 2016

Page 2: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenContents

1) The global carbon cycle on a geologic time scale

2) Soil carbon cycling and soil structure as affected by soil biota:

• Large Herbivores, bioturbating mammals

and termites

• Earthworms

• Roots, fungi and bacteria

Biogenic

aggregate

Page 3: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenRole of soils in the global carbon cycle

CO2 in atmosphere

780 Gt C (+3.3 a-1)Emission

6.3 Gt C a-1

Photosynthesis

120,7 Gt C a-1

Vegetation

600 Gt C

Respiration

60 Gt C a-1

Release

90 Gt C a-1

Uptake

92.3 Gt C a-1

Decomp.

60 Gt C a-1Litter

60 Gt C a-1

+ 0.7

Gt C a-1

Fossil

carbonSoil OM

ca. 3000 Gt COcean

39000 Gt C

Page 4: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenAtmospheric CO2 content over the last 40 million years

Zh

an

g e

t a

l., 2

01

3

The global cooling over the last 50 million years can be partly attributed to a

massive reduction of atmospheric CO2 content

Page 5: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenSoil carbon sequestration on a geological scale

The loss of atmospheric CO2 was mainly

caused by:

• lower subduction rates of carbonate-

rich marine sediments

decrease of volcanic outgassing

• mountain range formation

increase in rock weathering

Page 6: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenMycorrhiza: symbiosis of plant and fungi

with relevance for weathering

Reid (2001)

• Mycorrhizal fungi are ‘extention of

roots’

• Fungi deliver to plant water

and nutrients

Mycorrhizal fungi are involved in

OM decomposition

(ectomycorrhiza, EM) and

mineral weathering (EM and

arbuscular mycorrhiza)

• Plant supplies fungi with sugars

Page 7: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenRock eating fungi – mineral weathering by mycorrhizal fungi

van Breemen et al. (2000)

SEM micrographs

A) Roots and mycelia

on granite

B) Mycelia on weathered

granite

C) Hyphae penetrating

weathered feldspar in

granite

D) Interior of feldspar

grain

E) Hyphae associated

with feldspar grain

F) Hyphae associated

with quartz grain

Plant nutrition

Mineral weathering

Soil genesis

(Earth surface

shaping)

Page 8: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenMycorrhizal weathering of muscovite

Weathering of muscovite

by mycorrhizal fungi as

determined by confocal

laser microscope

Page 9: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenSoil carbon sequestration on a geological scale

The loss of atmospheric CO2 was mainly

caused by:

• lower subduction rates of carbonate-

rich marine sediments

decrease of volcanic outgassing

• mountain range formation

increase in rock weathering

• sequestration of carbon in soils,

e.g. grassland soils

Chernozem

(south Siberian steppe)

Page 10: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenSoil carbon sequestration on a geological scale

• The increasingly cooler, drier climate promoted the propagation of

grasslands, replacing the thermophilic forests that thrived in warmer,

more humid geologic eras

• By contributing to global cooling, the sequestration of carbon in

grassland soils played a role in further grassland expansion

Page 11: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

http://smallfarms.oregonst

ate.edu/sites/default/files/s

qn2013_gregretallack.pdf

From Retallack, G.:

Downloaded September

30, 2016

Stabilisierung organischer Substanz im BodenGrassland expansion and organic carbon sequestration

Retallack, G. (2013) Annual Reviews of Earth and Planetray Sciences 41, 69-86.

“Similarly, global expansion of grasslands and their newly evolved, carbon-rich soils (Mollisols) over the past

40 million years may have induced global cooling and ushered in Pleistocene glaciation. Grassland evolution

has been considered a consequence of mountain uplift and tectonic reorganization of ocean currents, but it

can also be viewed as a biological force for global change through coevolution of grasses and grazers.”

Page 12: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenSoil carbon sequestration on a geological scale

Sapristel

(lower Yenissei,

Siberia)

• The storage of carbon in soils has

been affecting the global climate

throughout the geologic past

• Besides grasslands, the largest

amounts of carbon are stored in

permafrost soils and peatlands

• Nowadays these soils are

turning into a carbon source!

Ruptic-histic Aquiturbel (Kolyma, Siberia)

Page 13: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenSoil carbon sequestration on a geological scale

Sapristel

(lower Yenissei,

Siberia)

• The storage of carbon in soils has

been affecting the global climate

throughout the geologic past

• Besides grasslands, the largest

amounts of carbon are stored in

permafrost soils and peatlands

Ruptic-histic Aquiturbel (Kolyma, Siberia)

Page 14: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenContents

1) The global carbon cycle on a geologic time scale

2) Soil carbon cycling and soil structure as affected by soil biota:

• Large Herbivores, bioturbating mammals

and termites

• Earthworms

• Roots, fungi and bacteria

Biogenic

aggregate

Page 15: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Regional to

profile scale

Profile to

millimeter scale

Millimeter to

micrometer scale

Stabilisierung organischer Substanz im BodenInfluence of biota on soil structure and SOM cycling

on different scales

Page 16: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenLarge-scale SOM impact by mega and macrofauna

The macrofauna affects OM cycling in soils

• Large herbivores

faster biogeochemical cycling of OM

• Termites

concentrate OM by re-allocation to their mounds

• Bioturbants

mixing of soil layers and thereby OM

Page 17: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

At the Pleistocene / Holocene transition, Siberian grass steppes disappeared and

were largely replaced by forest and moss tundra

Grazing pressure and fertilization by grazing megafauna (e.g.

Mammuthus) led to predominance of grasses in Pleistocene

Most species hunted to extinction by humans

Stabilisierung organischer Substanz im BodenEffect of large herbivores on soil OC sequestration

Tim Haines, 2000

Zimov et al. (1995); Zimov (2005)

Page 18: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenEffect of large herbivores on soil OC sequestration

Zimov et al. (1995)

Arid climate Wet climate

Productive speciesSTEPPE

Unproductive speciesTUNDRA

ClimateHypothesis

Dry Soils High Evapo-transpiration

High Soil Oxygen

High rates ofMineralization

High NutrientAvailality

High LitterQuality

Low Evapo-transpiration

Wet Soils

Low Soil Oxygen

Low rates ofMineralization

Low NutrientAvailality

Low LitterQuality

Page 19: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenEffect of large herbivores on soil OC sequestration

Zimov et al. (1995)

Productive speciesSTEPPE

Unproductive speciesTUNDRA

Dry Soils High Evapo-transpiration

High Soil Oxygen

High rates ofMineralization

High NutrientAvailality

High LitterQuality

LargeGrazers

FecesUrine

Surfacedisturbance

Lowdisturbance

LowHerbivory

HerbivoryHypothesis

Low Evapo-transpiration

Wet SoilsHumanHunting

Low Soil Oxygen

Low rates ofMineralization

Low NutrientAvailality

Low LitterQuality

Page 20: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenEffect of large herbivores on soil OC sequestration

Zimov et al. (1995)

Arid climate Wet climate

Productive speciesSTEPPE

Unproductive speciesTUNDRA

ClimateHypothesis

Dry Soils High Evapo-transpiration

High Soil Oxygen

High rates ofMineralization

High NutrientAvailality

High LitterQuality

LargeGrazers

FecesUrine

Surfacedisturbance

Lowdisturbance

LowHerbivory

HerbivoryHypothesis

Low Evapo-transpiration

Wet SoilsHumanHunting

Low Soil Oxygen

Low rates ofMineralization

Low NutrientAvailality

Low LitterQuality

Page 21: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im Boden

The macrofauna affects OM cycling in soils

• Large herbivores

faster biogeochemical cycling of OM

• Termites

concentrate OM by re-allocation to their mounds

• Bioturbants

mixing of soil layers and thereby OM

Large-scale SOM impact by mega and macrofauna

Page 22: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenTermites: Effects of carbon cycling

• Horizontal allocation of OM

• Termites concentrate and process OM in their mounds

Beckmann, 1987

Page 23: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenTermite mounds in Africa

Photos: Reinhold Jahn

Page 24: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenTermites: Effects of carbon cycling

Reviewed in Bonachela et al. (2015);

Siebers et al. (2015)

Tree-dominated mounds in Sofala,

Mozambique, taken from helicopter

(from Bonachela et al., 2015)

Termite mounds:

• promote water infiltration

• are enriched in OM and nutrients

Ecological hot spots

supporting rich plant

assemblages and the

associated animals, especially

relevant in dry seasons

Termite mounds buffer

ecosystems against

desertification

Page 25: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenTermite mounds: landscaping

Light detection and ranging

(LIDAR) hillshade image

of termite mounds in

South Africa’s Kruger

National Park

Termite mounds on

Bangweulu

floodplain, Zambi

Banchela et al. (2015)

Page 26: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenOrganic matter translocation and depodsolization by ants

Outside of nest Underneath

of nest

Underneath of nest

20 years after

abandonment

Kristiansen und Amelung (2001)

Page 27: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im Boden

The macrofauna affects OM cycling in soils

• Large herbivores

faster biogeochemical cycling of OM

• Termites

concentrate OM by re-allocation to their mounds

• Bioturbants

mixing of soil layers and thereby OM

Large-scale SOM impact by mega and macrofauna

Page 28: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenGrassland soils: Vertical OM allocation by bioturbation

• In steppe climates, there is an annual surplus of OM production

• In the moist spring months, more OM is produced by the vegetation than

can be decomposed in the dry summer and cold winter months

• Therefore, OM is enriching in soils and grasslands, thus becoming a

significant sink for atmospheric carbon dioxide

South Siberian steppe

Page 29: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenGrassland soils: Vertical OM allocation by bioturbation

The extension of grasslands into relatively moist

climate is enabled by large herbivores, which cause

a selective advantage of grasses over woody plants

wikimedia commons

• OM production is related to annual precipitation

• Transport of SOM by bioturbation

• Deep A horizons rich in OM

Page 30: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenGrassland soils: Vertical OM allocation by bioturbation

typical signs of

bioturbation:

Krotowina (russ.

Крот = mole)

(filled hollows of

burrowing mamals)

Page 31: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenGrassland soils: Vertical OM allocation by bioturbation

Ivanov and Khokhlova (2008)

Model profile of chernozem

Mean of 200 profiles from the central

chernozemic region of Russia:

1: 12C in % of soil (upper 10cm = 100%)

2: 12Cha in % of the soil,

3: 12C in % of Corg

Mean of radiocarbon datings from 46

samples:

4: 14C in 14Cha in % of the soil

5: MRT (mean residence time) in ka

6: K% of the soil

Increase in radiocarbon

age with soil depth

Page 32: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenDeep soil OM: more and older

Jobbagy and Jackson (2000)

Depth Global SOC stock (Pg)

0-1 m 1,300-1,600

1-2 m 500

2-3 m 350

Below 40 cm ~ 50%

Below 20 cm ~ 80%

Permafrost below 30 cm

>800

Relevance of OM translocation

to subsoil:

Globally, most soil organic carbon is below 50 cm, but only

few studies look below 30 cm

• Most deep soil organic

carbon is very stable

• Since we do not know

why it is stable, we

cannot predict

vulnerability to change

(Torn et al. 2009)

… but of course also other

processes contribute to organic

matter accumulation in subsoil

Page 33: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Regional to

profile scale

Profile to

millimeter scale

Millimeter to

micrometer scale

Stabilisierung organischer Substanz im BodenInfluence of biota on soil structure and SOM cycling

on different scales

Page 34: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenImportance of environment and biota for soil organic matter

Schmidt et al. (2011)

(plus bioturbation)

Page 35: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenEarthworm burrows

• Epigeics transform litter on the soil surface

• Endogeics ingest large amounts of soil; mostly horizontal burrows

• Anecics mix surface litter with soil; mostly vertical burrows

• Burrow walls: high OM content hot spots for microbial activity

• Burrows promote air and water infiltration into soils

Page 36: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenEarthworm burrows create hot spots

Tomography of

earthworm burrows

• Earthworm burrows are sites of high microbial activity (hot spots)

75

50

25

0

0 1 2 3

S.E.

soil carbon [% C]

soil matrix

preferential flow paths

depth

[cm

]

0 50 100 150 200 250

S.E.

Cmic

[mg kg-1]

soil matrix

preferential flow path

0 25 50 75

DNA [mg kg-1]

0.0 0.5 1.0

DAPI counts [1010

cells kg-1]

Parameters of microbial activity along

preferential pathwas

Bundt et al. (2001a, b)

H.-J. Vogel

Page 37: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenEarthworm casts

• Mixtures of soil and OM decomposed in earthworm guts

• Can be easily processed by bacteria and fungi

Earthworm activity increases the amount of bacteria and fungi

Royal Earthworm

Society of Britain

Page 38: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenEarthworm activity: Stabilization of organic matter

in aggregates vs. release of CO2

OM is protected in microaggregates

in casts, burrow linings, and middens

Lubbers et al., 2013

Earthworm activity leads to C mineralization

release of CO2, N2O

Page 39: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenImpact of earthworms on organic carbon stocks

Earthworm biomass correlates with OC stocks

Relationship between earthworm biomass

and total soil C across 16 farms in the

western Sacramento Valley, California

Furthermore, residue management options are relevant

Earthworm activity increases SOM

(Tomato) mulch

enhances earth-

worm acitivity

Fonte et al. (2009)

Page 40: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenEarthworm cast: indication of organic matter stabilization

• Earthworm casts are enriched in easily available organic matter

protected within aggregates

Size classes (mm) of water-stable aggregates of earthworm cast and

surrounding soil

Guggenberger et al. (1996)

Sample 8-5 3-3.15 3.15-2 2-1 1-0.5 0.5-0.2 <0.2

Earthworm cast 494 27 188 22 3 2 3

Surrounding soil 168a 222b 201 192c 100d 57e 56f

Casts Soil Casts Soil Casts Soil

Dry weight (g kg-1 soil) 415 406 272 159a 313 406b

C content (g kg-1) 35.0 2.8a 63.3 32.1b 57.8 43.0c

(ac/al)V 0.22 0.39 0.47 0.80 0.62 1.10a

(Hexoses/Pentoses) 0.52 0.28a 1.19 0.94 1.89 2.38b

Sand (0.2-2 mm) Silt (2-20 µm) Clay (< 2µm)

Characteristics of OM associated with earthworm cast and surrounding soil

Page 41: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substa nz im BodenBiogenic aggregates versus physiogenic aggregates

Fresh

cast

• Under pasture casts are enriched in fine particulate organic matter and

microaggregates mixed with fine materials

Earthworms can directly initiate the formation of microaggreagtes with

concomitant stabilization of organic matterPulleman et al. (2005)

Welded

cast

Intermediate

fractionPhysiogenic

aggregae

Impact of earthworm activity on soil macro- and microaggregates and OM

incorporation under different farming systes

Pasture 47.6 % 29.9 % 22.6 %

Conventional 7.4 % 25.5 % 66.0 %

tillage

Page 42: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Regional to

profile scale

Profile to

millimeter scale

Millimeter to

micrometer scale

Stabilisierung organischer Substanz im BodenInfluence of biota on soil structure and SOM cycling

on different scales

Page 43: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenMean residence time of different biomolecules

Schmidt et al. (2011)• No individual compound appears to be recalcitrant!

Page 44: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenChange in paradigm of organic matter stabilization

Schmidt et al. (2011)• Active stabilization of biomolecules is necessary

Page 45: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenStabilization processes of organic matter in soil

• Biota is involved in stabilization of OM by physical separation

and interactions with minerals

HOOC RbCC C

a g

BlackCarbon

Aliphatc Biopolymers Lignin

Physical separation Interaction with minerals

Chemical recalcitrance

200 nm

Page 46: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of biota in OM stabilization within aggregates

Bingham

et al. (2016)

The pathway from plant residue input over microbial decomposition processes

to spatial separation of OM in soil aggregates.

Page 47: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenConcept of formation of biogenic aggregates

Julie Jastrow

CONCEPTUAL DIAGRAM OF AGGREGATE HIERARCHYFrom Jastrow and Miller, 1998, In Soil Processes and the Carbon Cycle, CRC Press.

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphae

Plant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Plant root

CONCEPTUAL DIAGRAM OF AGGREGATE HIERARCHYFrom Jastrow and Miller, 1998, In Soil Processes and the Carbon Cycle, CRC Press.

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphae

Plant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Particulate organic

matter colonized by

saprophytic fungi

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphaeMycorrhizal hyphae

Plant and fungal debrisPlant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructuresClay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Microaggregates

~ 90-250 and 20-90 m

Plant rootPlant root

Page 48: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenMycorrhiza: symbiosis of plant and fungi

with relevance for soil aggregation

Reid (2001)

• Mycorrhizal fungi are ‘extention of

roots’

• Fungi deliver to plant water

and nutrients

Mycorrhizal fungi are involved in

OM decomposition

(ectomycorrhiza, EM) and

mineral weathering (EM and

arbuscular mycorrhiza)

• Plant supplies fungi with sugars

Parts of OM is fungal derived

Hyphaea together with plant

roots are enmeshing soil

particles, forming aggregates

Page 49: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenThe role of mycorrhizal fungi for soil organic matter

Glomalin (mg g-1

)

0 1 10

Ag

gre

gate

sta

bilit

y (

%)

-20

0

20

40

60

80

100

120

r2 = 0.86, p <0.001, n = 37

Y = 42.7 + 61.3 x log10

IREEG

Mid-Atlantic states

IllinoisTexas

MinnesotaScotland

Glomalin, a glycoprotein on hyphae

of arbuscular mycorrhizal fungi on

the surface of soil aggregates

(Wright, 2002)

Relationship between extractable glomalin

and water-stable aggregates (1-2 mm)

(Wright and Upadhyaya, 1998)

• Increases with soil age

• Has a mean residence time

of decades

• Represents 1-20% of SOC• AM fungi foster soil

aggregation

Page 50: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenAggregate formation: Role of soil fungi

(both saprotrophic and mycorrhizal)

Bacteria and fungi

on wheat straws

Fungal hyphaelinking soil particles

Chenu and Stotzky (2002)

Besides plant roots, fungal hyphae can play a significant role in binding soil

particles together to form larger aggregates

Page 51: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenAggregate formation: Role of fungi

Mean weight diameter (MWD) determined by fast

wetting (FW), mechanical breakdown (MB), and

slow wetting (SW) pre-treatments

Different letters indicate differences (p < 0.001)

Impact of residues and plants on aggregates

4 combinations: with/without plant growth (wheat)

with/without wheat residue addition

addition of residues and the

presence of plants with active

roots increased the presence of

all aggregation agents

most important aggregating

agents: Soluble carbohydrates

and fungal activity linked to

production of glomalin type

proteins

Carrizo et al. (2015)

Page 52: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenFormation of small microaggregates by bacteria

Chenu and

Stotzky (2002)

Cryo-TEM of bacterial microaggregate

Page 53: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenFormation of mineral-organic associations

Chenu and Stotzky (2002)

• Bacteria, minerals and OM can form mineral-organic composites

• Attachment of bacteria onto minerals can proceed via electrostatic attraction,

hydrophobic interaction, and by cellular excretions

• Microbial exudates increase aggregate stability

Page 54: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenSoil aggregates as analysed by TEMF

oste

r (1

98

8)

A, amoeba; B, bacteria; C, clay mineral(s); CW, cell wall; CWR, cell-wall remnant; F, fungal hypha (vesicular-arbuscular mycorrhizal?);

1t0, humified organic matter; M, mucigel; PP, polyphenols; P, pore; Q, quartz grain (site of); E, egg; FE, faecal pellet; L, lysis zone in mucigel

Page 55: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenEvidence of soil fauna and plant residues in soil aggregation

Left: Crack filled with excrements of Enchytraeidae;

Right: Organic residues in the aggregated soil matrix.

Dark-field illumination. Scale bar: 200 µm.

Rasa et al. (2012; thin sections and images by Thilo Eickhorst) University of Bremen

Soil Microbial Ecology

Dr. Thilo Eickhorst

[email protected]

Page 56: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Fluorescence microscopic ob-

servations of microaggregates

ReviTec site in

Ngaoundéré (Cameroon).

A: Microaggregate, consisting of very

fine organic and mineral material and

colonised by bacteria;

B: Fungi are part of microaggregates

C: Organo-mineral complexes

consisting of plant debris colonized by

bacteria.

#1: Fluorescent images after double

excitation

#2: Fluorescent images after UV

excitation for the visualization of DAPI

stained microorganisms.

Scale bar: 50 μm.

Schnee and Eickhorst (2016 in prep.)

Page 57: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenVisualization of microbial colonization

Soil aggregates (1-2 mm) packed at different bulk densities (1.3 g/cm³ left, 1.5 g/cm³

right) and inoculated with Pseudomonas fluorescens and Bacillus subtilis;

visualization of microbial colonization in the undisturbed soil matrix after DAPI

staining (blue dots) in polished sections after resin impregnation.

Juyal, Otten and Eickhorst (2016 in prep.)

Page 58: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenFISH-detected microorganisms in soil microaggregates

Left: FISH-stained bacteria (green dots) and autofluorescing fungal hypha and soil

matrix (red); right: FISH-stained fungi (green hyphae) and soil matrix (red).

CLSM images (maximum intensity projections of z-stacks). Scale bar: 50 µm.

Eickhorst (2016, in prep.)

Page 59: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenFISH-stained bacteria in soil microaggregates

Left: Microaggregate stabilized by fungal hypha (autofluorescence); Scale bar: 50 µm.

Right: Bacterial cluster colonizing a soil microaggregate. Scale bar: 20 µm.

Note: Images represent hot spots; a lot of similar aggregates were less colonized.

CLSM images (maximum intensity projections of z-stacks).

Eickhorst (2016, in prep.)

Page 60: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenBonding of minerals to bacteria

E. coli

Goethite

Montmorillonite

Kaolinite

Adsorption at edges,

not at basal surfaces

Almost no aggregate

formation

Tightly adsorbed at edges

and basal surfaces

In agreement with DLVO

(electrostatic & van der Waals

interactions)

Huang et al. (2015)

Page 61: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenMicrobial necromass as source of OMS

ch

urig

et al. (

20

13

)

Scanning electron micrographs of

soil particles (64 years; site 6) with

cell-envelopes

Soil development of the Damma glacier chronosequence

Coverage with bacterial fragments

C, N, C/N

C

N C/N

• Microbial cell-wall fragments are

an important soil organic matter

fraction

Increasing age

Page 62: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenAggregation at clay-sized scale:

Abiotic and biotic glues

100 nmA

B

Al

C

Si

Fe

Inte

nsity

A B

r2 = 0.95

r2 = 0.59

r2 = 0.25

TEM image with EDX spectra of a microaggregate from an

Umbric Andosol Bw horizon

• Soil dispersion often does not give true primary particles but microaggregates

• Not much is known about gluing agents: abiotic versus biotic

Mikutta et al. (2006)

Page 63: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRelevance of aggregate hierarchy for OM storage

OC concentrations and C/N and C/P ratios in differentaggregate size classes

• Larger aggragates contain more OC due to additional OM in

interaggregate space (= organic glue)

Soil Site Aggregate size OC [mg g-1] C/N C/P

Mollisol Native 2000-8000 µm 35 12 n.d.grasland 500-2000 µm 34 11 113Nebrasca 300-500 µm 30 10 99

208-300 µm 25 10 8490-208µm 24 9 8453-90 µm 20 9 74<53 µm 20 9 75

Alfisol Soybean 1000-2000 µm 23 11 n.d.Missouri 500-1000 µm 18 9 n.d.

250-500 µm 18 9 n.d.100-250 µm 22 8 n.d.<100 µm 12 7 n.d.

Alfisol Arable land 1000-4000 µm 24 16 n.d.France 250-1000 µm 14 11 n.d.

50-250 µm 11 12 n.d.<50 µm 7 9 n.d.

Co

mp

iled

by G

ug

ge

nb

erg

er

(20

02

)

Page 64: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRelevance of aggregate hierarchy for OM stabilization

Mean residence time of OC in macro and microaggregates ofdifferent ecosystems as assessed by the C4/C3 approach

• Microaggregates are efficiently stabilizing organic matter by

physical separation of the substrate from decomposing microorganisms

Ecosystem Aggregate µm MRT (yr)

size class

Temperate pasture Macroagg. 212-9500 140

Microagg. 53-212 412

Corn Macroagg. >250 14

Microagg. 50-250 61

Corn Macroagg. >250 42

Microagg. 50-250 691

Wheat-fallow, NT Macroagg. 250-2000 27

Microagg. 50-250 137

Wheat-fallow, CT Macroagg. 250-2000 8

Microagg. 50-250 79

Average ± SE Macroagg. 42 ± 18

Microagg. 209 ± 95

Co

mp

iled

by S

ix a

nd

Ja

str

ow

(20

02

)

Page 65: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenConcept of formation of biogenic aggregates

Julie Jastrow

CONCEPTUAL DIAGRAM OF AGGREGATE HIERARCHYFrom Jastrow and Miller, 1998, In Soil Processes and the Carbon Cycle, CRC Press.

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphae

Plant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Plant root

CONCEPTUAL DIAGRAM OF AGGREGATE HIERARCHYFrom Jastrow and Miller, 1998, In Soil Processes and the Carbon Cycle, CRC Press.

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphae

Plant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Particulate organic

matter colonized by

saprophytic fungi

Particulate organic

matter colonized by

saprophytic fungi

Mycorrhizal hyphaeMycorrhizal hyphae

Plant and fungal debrisPlant and fungal debris

Silt-sized microaggregates

with microbially derived

organomineral associations

Silt-sized microaggregates

with microbially derived

organomineral associations

Clay microstructuresClay microstructures

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Pore space; polysaccharides

and other amorphous

interaggregate binding agents

Microaggregates

~ 90-250 and 20-90 m

Microaggregates

~ 90-250 and 20-90 m

Plant rootPlant root

Page 66: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Fe

(III)SOM

Under reducing conditions: soil bacteria such as Geobacter spec.

dissolve iron oxides by using them as electron acceptors

Soil bacteria can dismantle aggregates cemented by iron oxides

Regelink et al. (2015)

Small microaggregates (1-10 µm)

• mostly controlled by Fe-(hydr)oxides,

smaller role of OM

• Fe-(hydr)oxides attached to clay and silt

adsorption sites for OM

Page 67: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Fe

(III)SOM

Schwertmann (1991), Lovley et al. (1998), Ryan and Gschwend (1990, 1992)

Under reducing conditions: soil bacteria such as Geobacter spec.

dissolve iron oxides by using them as electron acceptors

Soil bacteria can dismantle aggregates cemented by iron oxides

e-

Page 68: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Schwertmann (1991), Lovley et al. (1998), Ryan and Gschwend (1990, 1992)

Under reducing conditions: soil bacteria such as Geobacter spec.

dissolve iron oxides by using them as electron acceptors

Soil bacteria can dismantle aggregates cemented by iron oxides

SOM

Fe(II)

Page 69: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Schwertmann (1991), Lovley et al. (1998), Ryan and Gschwend (1990, 1992)

Under reducing conditions: soil bacteria such as Geobacter spec.

dissolve iron oxides by using them as electron acceptors

Soil bacteria can dismantle aggregates cemented by iron oxides

Significantly accelerated by

dissolved OM functioning

as electron shuttle

Fe

(III)

e-

SOM

DOM

Page 70: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Schwertmann (1991), Lovley et al. (1998), Ryan and Gschwend (1990, 1992)

Under reducing conditions: soil bacteria such as Geobacter spec.

dissolve iron oxides by using them as electron acceptors

Soil bacteria can dismantle aggregates cemented by iron oxides

Significantly accelerated by

dissolved OM functioning

as electron shuttle

Fe

(III)

e-

SOM

DOM

Fe

(III)

e-

Page 71: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Lovley et al. (1999)

Acceleration of microbial

(Geobacter metallireducens)

iron oxide reduction by soil

humic acids and AQDS, a model

quinone compound

Page 72: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

StabiConclisierung organischer Substanz im BodenRole of bacteria in aggregate destabilization

Lovley et al. (1998)

Soil aggregates cemented by Fe

oxides can be destabilized from

the inside by iron-reducing

bacteria

By using dissolved OM as electron shuttle, iron-reducing bacteria such as Geobacter can access Fe(III) and other metals occluded in tight pore spaces that they otherwise could not reach

Page 73: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenConclusions 1

1. Biota is responsible for the formation of organic matter

2. Further, it is responsible for the stabilization of organic matter

in soil, working at different scales

• Regional scale: Redistribution, acceleration of organic mattercycling and increase in soil fertility, creation of hot spots

• Soil profile scale: Input of organic matter into the subsoil(bioturbation, rhizosphere input), where organic matter is stabilized

• Aggregate scale: Active formation of aggregates with physicaldisconnection of substrate and decomposers

• Small microaggregate scale (there are not many individual particlesat clay-size scale): Active and passive formation of organo-mineral associations with binary and ternary complexes

Page 74: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenConclusions 2

Change of paradigm from dominance of non-targeted

abiotic processes in aggregate formation and organic

matter stabilization to a biotic control

With the formation of soil structure, biota is shaping its

soil environment according to its needs

Soil biota is much better soil engineer than we are!

Just compare the carbon stabilization by soil biota and

our efforts of climate-change mitigation

Page 75: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Thank you

Page 76: The interactions between soil biota, soil structure, and SOM … · 2016-10-31 · The interactions between soil biota, soil structure, and SOM dynamics Leibniz University Hannover

Stabilisierung organischer Substanz im BodenGroup tasks

1. In which ecosystems and how do large herbivores impact

soil organic matter and nutrients? Discuss also the role of

different densities of the animals.

2. Where in the soil do you expect hot spots and where cold spots?

What are the consequences for organic matter and nutrient

cycling?

3. How would you analyse the contribution of mycorrhizal fungi,

saprotrophic fungi and bacteria to aggregation and soil organic

matter storage?

4. Which processes may lead to the destabilization of organic

matter? (a) OM in permafrost soils; (b) OM in Mollisols; (c) OM

sorbed to pedogenic Fe-oxides; (d) OM in subsoil horizons. Hint:

In any case it must be associated with changing environmental

conditions.