Where next? Elizabeth Stockdale Slido: #B457 Biological Chemical - - PowerPoint PPT Presentation

Slido: #B457

Elizabeth Stockdale

Where is is soil research in in 2018? Where next?

Slido: #B457

Biological Physical Chemical

Slido: #B457

Plant residues Soil organic matter Earthworms Collembola Enchytraeids Bacteria Fungi Protozoa Bacterial feeding nematodes Fungal feeding mites Fungal feeding nematodes Predatory nematodes Predatory mites comminution

Food web interactions

Slido: #B457

Slido: #B457

Studies of impacts on processes

• Decomposition of organic matter
• Transformation of chemicals between forms
• Pesticide degradation
• Degradation of pollutants
• Association with plants (Rhizobia, mycorrhizae)
• Plant disease
• Biological control of plant pathogens
• Production of hydrophobic waxy compounds
• Formation and stabilisation of soil structure

Slido: #B457

Slido: #B457

SOIL LIFE

• There is lots of it
• Very species rich – still more to find

and identify

• Hangs out in hot spots
• High proportion dormancy
• Specialists – but lots of shared roles

Slido: #B457

Genes now key to identification

in soils, just as in crime drama…

Slido: #B457

microbial and genetic diversity

CO2 Inorganic N,P,S etc. Plant and animal residues

The microbial biomass concept

Soil

• rganic

matter

DNA and molecular methods

Detailed studies of genetic composition of whole population

Substrate utilisation, PLFAs

Detailed studies of the functional diversity of whole population

Microbial biomass

Whole nutrient pool, improved understanding

• f function, reduced

resolution.

Direct

• bservation

Total numbers but no understanding

• f functional roles.

Extraction and culturing

Detailed studies

• f a small part
• f the population

Slido: #B457

FYM/N NO N144

Broadbalk

Slido: #B457

• No Nitrogen
• 144 kg N ha-1 as NH4NO3 in spring
• 48 kg N ha-1 as NH4NO3 in spring

35 t ha-1 Manure in autumn

3 Plots: 3 Samplings:

• Before NH4NO3 application
• 3 days after NH4NO3 application
• 6 weeks after NH4NO3 application
• Pre-manuring
• Post-manuring

Experimental Design

Slido: #B457

Ammonium concentrations in soil

Pre-N 3d Post-N 6w Post-N mg N kg soil-1 NO N144 FYM/N 10 20 30 40 50 60 70 80 Pre-Man Post-Man

Slido: #B457

15 15N to determine rates of nit

itrif ification

Time

15N

Supply of soil 14N

Slido: #B457

Nitrification Rates

Pre-N 3d Post-N 6w Post-N NO N144 FYM/N Rate of nitrification (mg N kg-1 d-1)

1 2 3 4 5 6 7 8 9

Pre-Man Post-Man

Slido: #B457

Number of amo genes as determined by cPCR

Pre-N

FYM/N N144 N0 Copies of amo gene g soil-1

6w Post-N 3d Post-N

1 2 3 4 5 6 7 8

FYM/N N144 N0 FYM/N N144 N0 FYM/N N144 N0 FYM/N N144 N0

Pre-Man Post-Man

Slido: #B457

So what was learned about impacts of N fertilisation …

• Nitrification responds rapidly to ammonia addition; smaller

impacts of manures

• Population size changes more slowly
• Populations dominated by Nitrosospira in this arable system
• Roles for other ammonium oxidisers – Archaea?

Slido: #B457

So who and what … But where?

Slido: #B457

Location of microorganisms in soil

Protected from predators Food source available Accessible to nutrients and water Required oxygen gradient (anaerobic, aerobic)

Slido: #B457 Scanning Electron Microscope (SEM) 185 x 140 µm FOV X-ray analysis of silica

30 µm

NanoSIMS Silica 75 x 50 µm FOV (6 separate images)

10 µm

10 x 10 µm FOV NanoSIMS 15N/14N ratio of bacteria

Herrmann et al (2007) Rapid Communications in Mass Spectrometry 21, 29-34

Mapping location of microbial populations

Slido: #B457

0.00 0.05 0.10 0.15 1 2 3 4 Microns

f.

0.00 0.05 0.10 0.15 1 2 3 4 5 6 Microns

c .

2 micron

d. e .

2 µm

a. b.

Line-scan of 15N/14N across bacterial cells (1 micron dia.)

Clode, Jones, Kilburn, Stockdale, Herrmann and Murphy 2010

Organisms proliferate in the Rhizosphere

Slido: #B457

In Increasing detail of study of OM too…

moving away from extractions that change chemistry towards physical fractionation

Slido: #B457

Particulate:

• 5-20% soil C
• Partly decomposed

residues

• Supplies nutrients,

easily decomposed, rapid turnover

Particulate Soluble & suspended Pictures: Jeff Baldock, CSIRO.

Organic matter fractions

Soluble & suspended:

• 1%
• Dissolved in soil solution, compounds

with MW <1000

• Root exudates, humic material,

intracellular compounds

• Important microbial substrate

Minerals & microbial biomass Humus & Resistant

Slido: #B457

1 2 3 4 5 6 7 Non-amended soil Straw amended soil Gross N mineralisation (mg N kg-1 d-1) (b) * *

Cookson & Murphy (2004). Soil Biology and Biochemistry 36: 2097-2100.

Dis issolv lved (als lso calle lled solu luble) organic ic matter is is a mic icrobia ial food source

Experimental design:

• ± dissolved organic matter

Measured

• Nitrogen mineralisation
• Removing dissolved OM from soil

reduced Nitrogen mineralisation by microorganisms by 30-60%.

Whole soil DON leached

Slido: #B457

Conclusions

• Increasing detail in studies of soil…
• Increased understanding of soil biology and its role in soil processes
• Temptation to study microbial communities on their own (stamp collecting…)
• Temptation to study processes solely through molecular methods... If the

gene is there, if the gene is expressed…

• Still at scale of soil profiles, fields and farming systems, the scientists’

understanding of impacts on soil quality is incomplete and, where it does exist, fairly sketchy.

Slido: #B457

Email: elizabeth.stockdale@niab.com

Thanks to the organisers for the opportunity to present this work And thanks to lots of colleagues and collaborators over the years – especially: Dan Murphy, Christine Watson, Davey Jones, Keith Goulding