Amino acid

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Talk summary. • Basics of soil N ... Arctic. • New techniques for N tracing in the rhizosphere ... How much N is there stored in soil? ... What does this tell us about N cycling? ..... Intense competition exists between plants and microbes for nitrogen.

Nitrogen dynamics in the rhizosphere Modelling and experimental approaches

Davey Jones, Paul Hill, John Farrar, Mark Farrell, Paula Roberts, Liz Boddy, Liz York, Helen Glanville Kevin Newsham, David Hopkins, Tiina Roose, Andrea Schnepf, Richard Bardgett, Dan Murphy, Liz Stockdale, Matina Christou

Talk summary • • • • • •

Basics of soil N cycling Ecosystem scale models What types of N exist in soil Regulation of N cycling Rhizosphere scale models Examples – Antarctic – Europe – Arctic

• New techniques for N tracing in the rhizosphere

How many papers are there on soil nitrogen? In June, 2013: 251,357 papers Have we got enough information to model soil nitrogen well?

Using modelling as a tool to understand rhizosphere N flow …the last resort…..until recently

Soil nitrogen cycling “101” 1. How much N is there stored in soil? Soil (0-50 cm) = 5000 t /ha 5% soil organic matter = 250 t/ha C = 40%, C:N ratio = 12.5 Soil organic N = 8 t N/ha (8000 kg N/ha)

2. How much does a growing crop need? Yield 10 t/ha Grain N = 1.5% 150 kg N/ha/y

What does this tell us about N cycling?

Soil nitrogen cycling “101” 3. What is the main soluble form of N in soil? Soil water = 10 mg NO3- / l 5000 t soil / ha, 20% moisture =1,000,000 litres water/ha =10 kg NO3- / ha

4. What are the main inputs/outputs of N from soil? Inputs = rainfall, canopy throughfall, inorganic fertilizer, manure, roots & microbial death Outputs = leaching, runoff, gaseous losses (N2O, N2, NH3, NO3-)

Soil nitrogen cycling “101” 5. How much microbial N is there in soil? 1% of soil organic matter is microbial biomass 2.5 t biomass / ha 1.25 t microbial C / ha C:N ratio = 8:1 ≈150 kg microbial-N / ha

Soil microbial N in different land uses

Soil microbial N (kg N/ha)

Mean = 175 kg N/ha 1000

8000

600

400

300

Box/process modelling

Stella

Modelmaker

Crop N demand (150)

N2O, N2

Michaelis Menten kinetics V = (𝑉𝑚𝑎x . C C + Km )

Organic matter N (8000)

Soil water N First order kinetics

(10)

Microbial N (150)

V =k.C

𝐶 = 𝐶0 × exp−k.t … … .

NO3-

The Soil Nitrogen Cycle

DNDC: DeNitrification-DeComposition model

Previous work with DNDC

How good is the DNDC model?

Different crops, climates, locations, model versions

Variable climate data (East Anglia, UK) 500

25.0

450 20.0 400 350

250

10.0

200 5.0 150 100 0.0 50

Year

10

9

8

7

6

5

4

3

-5.0 2

0 1

Rainfall

300

Temperature

15.0

Different versions of DNDC: N2O emission prediction Version 82

Version 86

Version 90

Version 91

Version 92

Version 95

Different crops

Beet Peas Lettuce Beans Wheat Potatoes Brassicas

DNDC conclusions • Partly mechanistic model • Works well for maize in North Carolina • International acceptance

• • • • •

Parameter overload No validation in UK soils Changes in model not documented Needs ‘extra’ factors for other locations Implies our understanding of C and N cycling is poor

Back to the drawing board “Parameterisation and validation”

What forms of soluble N exist in soil?

Soil solution N in European soils

Citrus

Grasslands

Arable

Heathland

Vegetable

Wetland

Biofibres

Forest

Rank these in order of the type and amount of N present

Citrus

Grasslands

Arable

Heathland

Vegetable

Wetland

Biofibres

Forest

Soil solution N concentrations in European soils

Dissolved organic nitrogen (the forgotten N form in soil)

Where is the bottleneck in soil N cycling?

Protein  Peptides  Amino acids  NH4+  NO3-

Using modelling to determine rates of N cycling in soil Crop N demand (150)

Organic matter N (8000)

Soil water N (10)

N2O, N2

Microbial N (150)

NO3-

Isotope (14N, 15N, 12C, 13C, 14C) tracking in the field

Amino acid tracking in the field

DON quantified Soil solution removed

14C-15N-amino

acid added

Measure 14CO2 over time

Uptake into Plants (15N, 14C)

Soil samples

Inject back into soil

Uptake into microbes

Amino acid depletion from soil 𝑓 = 𝑎1 × exp−k1t + 𝑎2 × exp−k2t + 𝑎3 × exp−k3t Triple first order kinetic equation

14

C remaining in soil (% of total)

100

95

90

85

80

75

k1:T1/2 = 15 – 20 mins

70 0

5

10

15

Time (hours)

20

25

Amount of 14C recovered after 48 h (% of total)

Fate of amino acid-C in soil 60

50

40

30

20

10

0

CO2

Microbial biomass

Roots

Shoots

Amino acids Crop N demand (150)

Organic matter N (8000)

Soil water N

(0.3)

N2O, N2

Microbial N (150)

NO3-

Amino acid concentration =0.3 kg N/ ha Amino acid half life = 20 min Flux = 1300 kg N / ha / y

Turbocharged microbial biomass Soil solution amino acid pool turns over 4300 times per year

Where is the bottleneck in soil N cycling?

Protein  Peptides  Amino acids  NH4+  NO3-

60 14 14

50

C-Protein C-Amino acid mixture

First order kinetics

40

14

CO2 evolution (% of total

14

C substrate added)

Protein turnover is 50x slower than for amino acids

30

20

Non-first order kinetics

10

0 0

24

48

72

96

Time (hours)

120

144

168

Microbial peptide utilization is twice as slow as for amino acids Susbtrate utilization rate (nmol g-1 h-1)

400

Peptide Amino acid 300

200

100

0 0.0

0.5

1.0

1.5

2.0

Peptide or amino acid conc. (mM)

2.5

The main organic nitrogen degradation pathway in soil

50 SOM

Protein

2

Peptide

1 Amino acids

2 NH4+

NO3-

Block in acid soils

The bottleneck lies here (proteases)

How can we use this information? CO2

Soil respiration

0 Amino acids

Peptides

Adenosine Nucleoside

Amino sugar

2

Glucosamine

4 Carbohydrates

6

Sucrose

Glucose

Fructose

Valine

Tyrosine

Phenylalanine

Lysine

Leucine

Isoleucine

Glycine

Glutamine

Aspartic acid

Arginine

Alanine

Peptides

Organic acids

Field 2009 Field 2010

Succinic acid

Shikimic acid

Salicylic acid

Oxalic acid

Malonic acid

Malic acid

Glutamic acid

Formic acid

8

Citric acid

Acetic acid

% substrate C contribution to respiration

Mathematical modelling of the importance of dissolved organic C and N in soil respiration

=

Pool size x Flux = Importance

Plant N uptake

The historical view of plant nitrogen acquisition Protein Soil microbes

Soil particle

Peptides

Amino acids

Deaminase

NH4+

NO3-

NH4+

Peptidase

Most N enters soil as protein, which is modified by soil microorganisms until available to plants as inorganic N

Protease

Root

It is now widely accepted that plants can take up nitrogen earlier in protein decomposition Protein Soil microbes

Soil particle

Peptides

Amino acids

Deaminase NH4+

NO3-

NH4+

Peptidase

In some environments, plants can compete successfully with soil microbes for amino acids

Protease

Root

Both plants and soil microbes possess transporters for small peptides. Peptide uptake is energetically favourable

Peptide R F VK K GV

Extracellular medium

R

R F VK K V G R

Cytoplasm

But is this of any significance to the terrestrial nitrogen cycle?

The maritime Antarctic

Signy Island South Orkneys 60º43’S 45º36’W

Antarctic soils

Bare

Higher plants

Penguin colonies

Lichens

Bryophytes

Algae

Higher plants

Extensive carpets of moss with large stocks of proteinaceous organic matter

Over the last 50 y some areas of the maritime Antarctic have warmed almost an order of magnitude faster than the global mean with a concurrent expansion of vascular plants Guglielmin et al., 2012

Over the last 50 y some areas of the maritime Antarctic have warmed almost an order of magnitude faster than the global mean with a concurrent expansion of vascular plants

2°C change

Guglielmin et al., 2012

D. antarctica is often found growing in competition with mosses especially Sanionia uncinata

Both plants have temperature optima for photosynthesis above current maritime Antarctic summer temperatures.

But nutrients are needed to exploit temperature rises

Unlike mosses D. antarctica has roots which penetrate into the organic matter stored in the soil

ca.20% of the soil soluble N pool under grass and moss is small (