Nematology in the provision of soil ecosystem services: nutrients and energy in the soil food web

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Nematology in the provision of soil ecosystem services:

nutrients and energy in the soil food web

Teagasc,

Environment Research Centre, Johnstown Castle,

Wexford.

bryan.griffiths@teagasc.ie

Bryan Griffiths

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Acknowledgements

Jane Davidson Fiona Brennan Jen Kennedy Vincent O’Flaherty Susan Mitchell Xiaoyun Chen

Dave Roberts Tim Daniell Jane Wishart Roy Neilson

Michael Bonkowski Nanjing Agricultural Uni.

SCRI sequencing service Christine Hackett, BIOSS

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Date for your diary

 2^nd International workshop on nematodes as environmental indicators

 5-6^th July 2012

 Ghent, Belgium

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Scope of presentation

 Ecosystem services is the new catchy title. Encompasses:

nutrient cycling; carbon sequestration; provision of clean water; disease suppression.

 This talk will concentrate on interactions in the food web

 And large-scale applications of nematode community structure

 Firstly, a reminder of the soil food web……

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Below-ground biomass = 600 sheep haHow many ‘sheep’ below-ground? ^-1; 1-2 tonnes ha^-1 Fauna 10% biomass = 60 sheep ha^-1; 1-200 kg ha^-1

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The soil food web

(de Ruiter et al. 1993, J Appl Ecol 30, 95-106)

Roots

Phytophagous Nematodes

Predaceous Nematodes

Predaceous Mites

Predaceous Collembolans Nematode

Feeding Mites

Detritus

Bacteria

Bacteriophagous Nematodes Bacteriophagous

Enchytraeids

Mites

Flagellates

Amoebae Saprophytic

Fungi

Collembolans

Noncrypto- stigmatic Mites

Cryptostigmatic Mites

Fungivorous Nematodes

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The soil food web - energy flows

Roots

Feeding Mites

Detritus

Bacteria

Enchytraeids

Mites

Flagellates

Fungi

Collembolans

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Carbon and nutrients essentially similar in terms of flow through the food web

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Ecological efficiency drives nutrient recycling

Nematodes have lower efficiencies (ca. 10%) than protozoa (ca. 40%)

Nematodes Protozoa

1 g increase in

biomass

Ingest 13 g bacteria Ingest 3 g bacteria

Excrete 0.9 µg N Excrete 0.09 µg N

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But not the whole story…

 If plants are grown with excess nutrients (i.e. no nutrient limitation), fauna still increase plant growth

 Recent research has related presence of protozoa to increased number and length of roots

 Due to grazing-stimulated production of plant hormones by rhizosphere bacteria

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Conceptual model of protozoan effects on root growth

Bonkowski & Brandt 2003; Bonkowski, 2004 New Phytol. Tansley review

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Generation of nematode-enriched soil

5µm mesh 1mm mesh

Mao et al., Soil Biol Biochem 2006; 2007

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27.8 ± 2.8 nematodes g^-1 soil 135.1 ± 13.1 nematodes g^-1 soil

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Plant growth experiment

Tomato seed

5µm 1mm

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Nematode treatments

Treatment

1mm 1mm mesh, 135 nematodes g^-1

5m 5 mm mesh, 27 nematodes g^-1

CE 5 m mesh + 135 C.elegans g^-1

Mixed 5 m mesh + 135 mixed nematodes g^-1

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Auxin (IAA) content of nematode-enriched soil

0 25 50

1mm 5um C.elegans Mixed nematodes

0 5 10

μg g^-1 dry soil

DAYS

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Plant root growth in nematode-enriched soil

30 40 50

1mm 5um "+Ce" "+Nem"

20 30 40 50

1mm 5um "+Ce" "+Nem"

a b a a

Root length (cm) Root tips (number)

1mm 5m CE Mixed 1mm 5m CE Mixed

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Molecular signals detected in plant roots

Valentine et al., in prep

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Conclusions

 Bacterial-feeding nematodes contribute to root development.

 Future work will try to identify the ‘genetic control points’.

 Long-term aim to manipulate nematode populations and root growth in the field.

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Bacteria fight back – 2^o metabolite repression

Neidig et al 2011 Microb. Ecol 61:853

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The soil INTERACTION web

Roots

Feeding Mites

Detritus

Bacteria

Enchytraeids

Mites

Flagellates

Fungi

Collembolans

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Molecular Biology for ecological studies

 Moving ahead rapidly, due to economic

implications of plant-parasitic forms and the Caenorhabditis elegans genome project.

 Micro-arrays available for plant pathogens.

 Many labs working on non-pathogenic forms and information readily available on the web.

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Aims

 Develop a molecular method of profiling soil nematode communities (because traditional methods too time-consuming and skilled)

 Validated against current techniques

 Apply the methods in an agricultural context, relating to effects of fertilisation.

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Nematode morphology

•A skilled job

• Takes a long time

• Would analysis of DNA be faster

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Molecular approaches

Amplify SSU Extract DNA

Sieve from 200g soil

48 hr Baermann funnel extraction

Bead beat &

kit purify

PCR

amplification of SSU

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Molecular approaches

Amplify SSU Extract DNA

Clone & sequence

phylogenetics

T-RFLP

Directed T-RFLP

T-RFLP advantages

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Directed T-RFLP – peaks related to trophic group

 Trace and pictures

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Long-term effects of P fertilisation

The study area was in South East Ireland, on which a long-term trial to study P for beef production has been carried out since 1968, with changes since 1999.

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P applications

Year

Treatment (kg P ha^-1 yr^-1)

1 2 3

P0 P15 P30

1968-1998 0 15 30

Year

Treatment (kg P ha^-1 yr^-1)

1 2 3 4 5 6

P0 P0-30 P15 P15-5 P30 P30-0

1968-1968-19981998

1999-2009

0 0

0 0 1515 1515 3030 3030

0 30 15 5 30 0

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Nematode abundance marginally affected

b b b ab

a b

ab abc bc

abc a

c

b b a

b b

b

0.0 5.0 10.0 15.0 20.0 25.0 30.0 35.0

P0-0 P0-30 P30-30 P30-0 P15-15 P15-5

NematodeNumbers(/gDrysoils)

Large(>125µm) Small(125-53µm) total

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Morphological – channel ratio increases with P

c

b

a a a a

60 65 70 75 80 85 90

P0-0 P0-30 P30-30 P30-0 P15-15 P15-5

NCR(%)

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Molecular – bacterial-feeders increase with P

40 50 60 70 80 90

0-0 0-30 30-30 30-0 15-15 15-5

%bacterial-feeders

a

b a,b

b

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Morphological vs Molecular

c

b

a a a a

60 65 70 75 80 85 90

P0-0 P0-30 P30-30 P30-0 P15-15 P15-5

NCR(%)

40 50 60 70 80 90

0-0 0-30 30-30 30-0 15-15 15-5

%bacterial-feeders

a

b a,b

b b

Time required:

9 days vs. 2 days

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Summary and future work

• Primers allow us to amplify SSU of main soil nematode types. Validated with traditional techniques.

• Directed t-rflp designed and tested in silico and on environmental samples

• Need to understand the differences in results

between morphological and molecular approaches

• Still some work to do but could be used to target samples for morphological analysis

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New projects include novel techniques

 European Commission funded project:

 Soil ecological function and biodiversity across europe

 www.ecofinders.eu

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To link:

biodiversity – function – ecosystem services

 Not just nematodes:

 Archaea, bacteria, fungi, protozoa,

nematodes, micro- arthropods, worms

 + functions: C cycling, N cycling, water

retention.

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A range of soils, climate and land use

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The benefits of large-scale studies:

An example from The Netherlands

Mulder et al. 2011 Advances in Ecological Research Vol. 44:

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Nematode response to livestock intensity

Mulder et al., 2005 Naturwissenschaften

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Thank you

Thank you…… Future directions:

More of the same!

Research on a broad front – applications of new techniques; above-ground below-ground interactions;

theory; interactions within the food web

National monitoring schemes increasingly important (especially in Europe)

Development of trait based approaches

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Trait differences

Heemsbergen et al 2004 Science

Significant trend

-20 -10 0 10 20 30

3 6 7 9 11 12 13 16 18

Functional dissimilarity

Netdiversityeffect

No trend

-10 -5 0 5 10 15

2 4 6 8

number of species

Netdiversityeffect

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Indices based on c-p and other traits have facilitated ecological studies

Ferris, Bongers, de Goede (2001) A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Applied Soil Ecology 18: 13-29

Bongers, T., 1990. The maturity index: An ecological measure of environmental disturbance based on

nematode species composition. Oecologia 83, 14-19.

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Form and function: Metabolic footprints of nematodes in the soil food web

Howard Ferris

European Journal of Soil Biology 46 (2010) 97-104

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Form and function: Metabolic footprints