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Soil Mesofauna Field Studies Council, Juniper Hall, February – March 2013
Welcome
• Domestics – fire, accommodation etc.
• Course objectives
• Your tutors
• Course timetable
• Questions?
Course Objectives
• Appreciate the range, ecology and function of soil organisms
• Get to know a range of water-dwelling soil organisms
• Be able to identify nematode functional feeding groups (trophic guilds)
• Understand springtails anatomy and ecology.
• Be able to identify springtails to species.
• Understanding mites anatomy and ecology.
• Ability to identify soil mites to family level.
• Know how to collect, handle and preserve soil mesofauna.
• Develop your microscopy skills
• Understand how soil mesofauna are monitored, recorded, and explored using genetic techniques
• Appreciate the range of ID resources available and where to get help and support.
• Develop links with other soil mesofauna people
Who we are:
• Dr Matthew Shepherd: Soil biodiversity specialist, Natural England – overview, help and general dogsbody!
• Dr Felicity Crotty: Soil Invertebrate Research Scientist, Aberystwyth University
• Dr Peter Shaw: Senior Lecturer in Biosciences, University of Roehampton
• Pete Boardman: Invertebrate Challenge Project Officer
Course Timetable
Friday 27th March – Introduction, Soil Life, Microscopes
• 12:00 Arrive, check-in etc
• 13:00 Introduction to the course, content and domestics
• 13:15 Introduction to soil biodiversity and ecology
• 14:15 Field collecting of soil/litter mesofauna
• 15:45 Tea
• 16:00 Tullgren funnels, microscopes, and ID of broad groups of mesofauna.
• 19:00 Dinner
• 19:45 Recording, resources and support networks – Pete Boardman
• 20:30 End
Course Timetable
Saturday 28th March – Collembola Day
• 09:00 Introduction to Collembola – Dr Peter Shaw
• 10:00 Field collection – vaccuum sampling
• 11:00 Coffee
• 11:30 Entomobryomorpha (talk and practical)
• 13:00 lunch
• 14:00 Entomobryomorpha contd.
• 15:30 Symphypleona (talk and practical as above)
• 16:15 Tea
• 16:30 Poduromorpha (talk and practical as above)
• 18:00 Dinner
• 19:00 Nematodes, moss piglets and other soil water beasties
• 20:00 End
Course Timetable
Sunday 29th March – Mites
• 09:00 Introduction to Acari - Dr Felicity Crotty
• 10:30 Mesostigmata – talk and practical session
• 11:30 Coffee
• 11:45 Mesostigmata - continued
• 13:00 Lunch
• 14:00 Oribatida (including Astigmatina) – talk and practical session
• 16:30 Prostigmata – talk and practical session
• 18:00 Dinner
• 19:00 Monitoring soil mesofauna and genetic barcoding
Course Timetable
• Monday 30th March Meso-Mini-Bioblitz
• 09:00 The morning’s challenge – to identify, quantify, record, all soil mesofauna from a complete soil core (or 2!)
• 11:15 Coffee
• 11:30 Plenary and feedback
• 12:00 Depart
Any questions or problems?
• Matthew – 07866 680786
• FSC contact….
Introduction to Soil Biology
Soil Biology
• What is soil?
• Soil organisms – a tour
• What soil life does for us
• What we do to soil life
• Conservation of soil biodiversity
Soils – the beginning...
Image: reconstruction of first land plants in ordovician, Jose Bonner CC BY-SA 3.0 Drawings: Aberdeen University after Scourfield (1940a, b) and Hirst 1923
Photos: M Shepherd
What is soil?
Photo: Matthew Shepherd
Soil Organisms • Organisms living entire life in soil?
• Many groups have above-ground lives too!
• Include litter, dead wood, standing dead wood?
• Dirt – what accumulates when you don’t clean!
• Useful to divide soil/non soil organisms?
• In practice “soil organisms” are the neglected ones!
Biomass and numbers
Image: Karl Ritz, Cranfield University
In a handful of
soil...
Image: Karl Ritz, Cranfield University
HEXAPODS
Biomass and numbers
Photo: Matthew ShepherdPhoto: Matthew Shepherd
• Huge diversity - soil is home to ¼ of all species on earth
• Soil biologists frequently group organisms in terms of their broad function:
– Chemical Engineers
– Biological Regulators
– Ecosystem Engineers
Types of Soil Organisms
Soil Organisms
• Chemical Engineers
– Break down organic materials
– Fix nutrients
– Tend to be tiny
– Influenced by small-scale factors
– Can be quick to respond to management
Soil Organisms
• Biological Regulators
– Influence other soil organisms through trophic processes
– Turn organic matter into dung – humus.
– Affected by larger scale factors (eg cow pat, plant litter)
– More stable numbers (months/years)
• Microfauna : protozoa, nematodes, rotifers, tardigrades...
• Mesofauna: hexapods, mites, isopods, myriapods.
Soil Organisms
• Ecosystem Engineers
– make large-scale changes in soil
– Moving, breaking down or aggregating soil and organic matter
– Digesting and excreting soil
• All 3 types interact to influence soil structure and function
Some ecological principles for soil
• Variable over very short distances and times
• High habitat heterogeneity = high biological diversity
• Adding resources seems to increase diversity – by increasing heterogeneity?
• Many soil organisms show widespread distributions – driven by resource, rather than dispersal
– “Everything Is Everywhere” and “The Environment Selects”
• High “background” diversity – dormant organisms waiting for a break…
• Lots seem to do the same job – functional redundancy – is biodiversity important?
Soil Organisms
Plants
• Plants are soil organisms too!
• Roots break up soil structure and enlarge pores
• Plant-fixed C is sole energy source driving the whole system
• litter from above and below ground
• roots – exudates
• Soil organisms also a major influence on plants...
Bacteria
Myxobacteria photo: Michiel Vos doi:10.1371/journal.pbio.0030398
Photo: Julia Plotnikov
Firmicutes Photo: Wikimedia commons
Photo: GrahamColm at en.wikipedia
Bacteria & Archaea • Tiny chemical engineers • Rapid reproduction - can make use of
sudden resource availability • Dormancy • Form biofilms • Hate fungi • Team up with plants
Fungi • Long hyphae through
soil – long distances and large volumes
• Damaged by disturbance
• Reproduction can be slow
• Energy efficient – like tough energy sources
• Hate bacteria • Team up with
plants...
Photo: Matthew Shepherd
Ectomycorrhizae
Arbuscular Mycorrhizae
Protozoa
• Single celled eukaryotes.
• Predators of microbes
• Aquatic – swim with cilia or flagella, or just ooze!
• Bioindicators – if you can ID them!
• Testate amoeba fossils can indicate past hydrology in peats.
Nematodes
• 28,000 species described – 441 soil species in UK
• Swim through soil water
• Different mouthparts indicate feeding strategy – “trophic guild”
• Can feed on roots, fungi, bacteria, organic matter or other soil organisms - can be pests, or control them
• Good indicators of microbial biomass?
Rotifers and Tardigrades
• Microscopic multicellular organisms in soil water
• Both can dry out completely then “come back to life”
• Rotifers swim or loop through soil – no sex for 40 million years!
• Tardigrades – “moss piglets” - 8 legged, tough – picked on by scientists!
Acari -Mites
Springtails - Collembola
Coneheads (protura)
Bristletails (diplura)
Thrips
Booklice (psocids)
Pseudoscorpions
Pauropods
Symphyla
Beetles
And the rest...
Flies
Photo: Michel Vuijlsteke
Isopods
• ~37 spp. in the UK –not just wood
• Vernacular names
• Can be major decomposers of soil organic matter
• Crustaceans – now joined by land amphipod
Myriapods
Photo: B Kimmel at nl.wikipedia
Ecosystem Engineers – Worms
• Big (earthworms) and little (enchytraeids)
• Enchytraeids like acid organic soils, most earthworms prefer neutral/basic
Earthworms
Epigeic Endogeic
Anecic Compost worms
Earthworms
Vertebrates
• Moles, rabbits, voles, badgers also major engineers of the soil
• Kingfishers, toads, lizards
• The vertebrate with the greatest impact on soil is...
Us!
What do we want from our soil?
Photo: waterboards.ca.gov
Photo: Tom Powers, University of Nebraska Lincoln
Policy Background – Ecosystem Services
Soil on strike?
Policy Background – Ecosystem Services
Soil’s Work • “the biological engine
of the earth”
• Engines need fuel…
Illustrations: Matthew Shepherd
What does the soil do?
• Plant carbon is the fuel
• Soil organisms are the engine…
Illustrations: Matthew Shepherd
Soil structure
Moving
Eating
Painting
Sewing Gluing
Photo: Matthew Shepherd
Photo: Joseph Morton, West Virginia University
Photo: Matthew Shepherd
Image: Karl Ritz, Cranfield University
• Most soils wouldn’t have structure without soil life
• How? Like a morning in a playgroup!
Soil structure
Wright, S. F. et al. Changes in Aggregate Stability and Concentration of Glomalin during Tillage Management Transition Soil Sci. Soc. Am. J. 1999. 63:1825–1829.
Decomposition AND C storage?
Decomposition…
CO2
CO2
CO2
… and C storage… and water retention
Water Infiltration
Smashed and structured
Drainage
• Bioturbation provides resilience to compaction
• Earthworm burrows can be important drainage feature – 2m deep!
• Loss of deep-burrowing worms can double runoff
Soil Function
• Water retention and release?
– Deeper root penetration
– Humus
– Mycorrhizal fungi
Soil Function
• Nutrient cycling and storage
– Right time – spring and autumn
– Right place – near the roots
C N
C N
C N
C N
C N C
N
Nutrient Release
What we do to them
• Low inputs of C to soil = no fuel to support soil life.
• Disturbance – kills big ones, and causes loss of soil C
• Compaction – less space to live and air to breathe!
• Erosion/building over – total habitat loss!
• Soil life is tough!
Soil structure • Most soils wouldn’t have structure without soil life
• How? Like a morning in a playgroup!
Moving
Eating
Painting
Sewing Gluing
Drainage
• Soil structure contributes to drainage
• Bioturbation provides resilience to compaction
• Permanent anecic burrows can be important drainage feature – 2m deep!
• Loss of anecic worms can double runoff
Crop pest control
What the soil biota do for us…
• For most of agriculture’s history soil biota gave us nutrients, pest control, and maintenance of soil structure.
• Technology now replaces their function – increasing agricultural productivity
• What does this do to the soil biota?
… and what we do to the soil biota...
• Rotations, monocultures monocropping very unlike natural situation where soil life evolved
• Modern crops bred without mycorrhizae – can resist colonisation
• Ploughing
• destroys fungi (incl. mycorrhizae)
• Breaks open aggregates to lose soil C
• Reduces weeds – also their C inputs, litter, exudates, mutualisms…
• kills larger worms (poorer infiltration = more runoff)
• Less mixed farming – less manure – less fuel for soil processes
• Erosion
- Habitat destruction
• Compaction
- Limits the space where organisms can live
• Pollution
- Toxic conditions for most soil organisms (there’s nearly always some that can survive...)
• Sealing (development)
- destroys biota, and future potential!
… and what we do to the soil biota...
Looking after life in the soil
• Soil life evolved alongside diverse natural plant communities
• Can we make soil work better by making agricultural soils more like natural ones?
• Characterised by:
– Higher soil organic matter (higher C)
– Lack of regular disturbance
– Diverse plant communities
Soil organic matter = More soil life
Source: Natural England, ECBN data, 2011-2013
y = 395.32ln(x) - 491.93 R² = 0.8434
0
200
400
600
800
1000
1200
1400
1600
1800
0 20 40 60 80 100
Tota
l So
il P
LFA
co
nte
nt
nm
g-1
% Soil Organic Matter (Loss on Ignition)
Soil organic matter and total soil PLFAs
Soil organic matter = better soil structure
y = -0.433ln(x) + 1.5756 R² = 0.5348
0.00
0.20
0.40
0.60
0.80
1.00
1.20
1.40
1.60
1.80
0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00
Bu
lk d
en
sity
g/c
m
% organic carbon (Walkley-black)
Grassland soil organic carbon and bulk density in England and Wales
Source: ADAS, Defra project BD5001
Soil organic matter = better drought resistance
Source: Countryside Survey, 2007
y = 21.517ln(x) - 12.746 R² = 0.8866
-20
0
20
40
60
80
100
120
0 20 40 60 80 100
% S
oil
wat
er
con
ten
t
% Soil Organic Matter
GB soil organic matter and soil moisture content
Soil organic matter = better nutrient retention
Source: Countryside Survey, 2007
y = 30.422ln(x) - 37.506 R² = 0.6967
0
20
40
60
80
100
120
140
0 20 40 60 80 100
Cat
ion
Exc
han
ge C
apac
tity
(m
Eq
10
0g_
1
% Soil organic matter (loss on ignition)
Soil organic matter and cation exchange capacity
Big improvements
in soil function due
to small increases
from low SOM
Soil organic matter
• Raise organic matter - put more in, or lose less
• Add more organic matter from elsewhere
• Grow more plants!
• Lose less organic matter -
• Min or no-till soils have more SOM in topsoils, larger aggregates containing more SOC and more N
• Pattern of SOM is changed – total increases only after a long time.
• Better for earthworms – more deep burrowing and surface-active, and fungi.
*Alvarez, 2006. Soil Use and Management, 21
Looking after life in the soil
• Rotations
• Multicropping – several crops same place & time
– Ryegrass & clover to Agroforestry
– More worms, diverse organisms
– SOM increase – trees
– Other plant nutrient/pest benefits
Photo Martin Wolfe, Wakelyns Agroforestry
Looking after life in the soil
• EC has been active: • European Atlas of Soil Biodiversity • Soil biodiversity: functions, threats and
tools for policy makers
“Soil biodiversity is neglected even amongst
conservationists. Despite representing
almost a fourth of the total biodiversity on
earth, soil organisms represent only 1% of
the IUCN red-listed species... This is not
because soil species are not endangered, but
because their status is overlooked.”
Conservation of Soil Biodiversity
• Biodiversity 2020 is main current driver in England
– Action for species
– Monitoring with volunteer/public involvement
– Biodiversity strategy indicators
– Tools to secure best value from ecosystems
– Mostly for current priorities?
Conservation of Soil Biodiversity
Conservation of Soil Biodiversity
• Conservation is driven by priority habitats and species.
• Data collected - rarity, measured decline, known habitat
loss
• IUCN conservation status: Near-Threatened,
Vulnerable, Endangered or Critically Endangered
• “Features” added to UK priority lists
• “Condition” defined and monitored
• Action plans drawn up and exectuted
• Can this apply to soil organisms?
• Soil fauna
monitoring data
sparse
• Even common
species look
rare!
Conservation of Soil Biodiversity Conservation of Soil Biodiversity
Conservation of Soil Biodiversity
• Workshops in 2012 and 2014 to develop ideas for
conservation of soil biodiversity
• Key actions
• Build soil biodiversity community in UK
• Develop tools for land managers to understand soil life
• Demonstrate, monitor and research practical farming
for soil life – all farmers are livestock farmers
• Improve communication of soil biology: beauty,
interest, importance
• Develop genetic approaches for understanding soil life
• Increase expertise and improve recording
Improving knowledge - Recording
• Few recording schemes
• Springtails – scheme
run by Peter Shaw
• Earthworms – E.S.B.
• Nothing yet for mites –
Scratchpad…
• National Biodiversity
Network
• More recorders and
more records!
Improving knowledge - resources
• Excellent FSC keys – springtails, woodlice, worms, centipedes.
• Other groups lack accessible keys – diplura, symphyla, protura, tardigrades etc.
• Developing a key for mites with FSC
• Some groups taxonomically uncertain!
• Species records are needed… can genetics help?
• Online tools... i-Spot, NBN, Flickr, Facebook
• https://www.facebook.com/#!/groups/438740999565613/
• Soils life is now more accessible than ever
– Microscopes cheaper than binoculars!
– Digital images/video through USB links to computers
– Ideal for armchair Naturalists...
• And is soil life really uncharismatic?
Improving knowledge & Recording
Thank you
Hope you enjoy the course!
Fieldwork!
• Mission: collect live mesofauna in the field!
– Sieve and pooter mesofauna from various habitats
– Collect standard soil cores for extraction
– Set up Tullgren funnels to extract mesofauna
• Before we go
– 1. Make a pooter – label it!
– 2. Get sieve, tray, collecting pots – labels!
– 3. Wellies and coats?
– 4. Health and safety – washing, gloves, adders, kneelers etc.
Nematodes and other soil
swimmers Matthew Shepherd, with thanks to Dr Roy Neilson and Sina Adl
• Many borderline meso/micro fauna in soil inhabit soil water
• Protists
• Nematodes
• Tardigrades
• Rotifers
• Most eat bacteria, fungi, each other, and each other’s excreta
• Nematodes – specific feeding strategies
Nematodes and Soil Water Fauna
• Protists in soil include ciliates and flagellates
• Ciliates - swim, or parasitic.
• Flagellates include amoebe, cercozoa, and us!
• Amoebe may be testate (in shells) – useful macrofossils, or naked
• Cercozoa – very common, but an be hard to see
• Slime moulds
• Selective foragers on bacteria, eaten by “bacterivore” and other nematodes and collembola.
Protists
• Useful bioindicators? Soil moisture, oxygen status, etc.
• Much affected by soil disturbance – take years to recover (25 years to be half way to forest), stress tolerant early species followed by competitive species.
• Build up of plant and organic matter can increase diversity
• 16,000 species are probably a quarter of true number
• 300? <600 in soil?
• Cosmopolitan – suggests wide dispersal
Protozoa
Protozoa
Testate Amoeba
Cercozoa
Slime Moulds
https://www.youtube.com/watch?v=BZUQQmcR5-g https://www.youtube.com/watch?v=5h8WOWEqP6o
Nematodes
• Nematodes are everywhere!
• “Worms” in dogs, children etc...
• Largest is 28m long – 1 going extinct soon...
• Also freshwater, marine and soil
• Soil bacterivore (Caenorhabditis elegans) first ever animal to be fully sequenced
Nematodes
• 28,000 spp. (16,000 are parasitic)
• Hugely important
• Some ecosystems - nematodes account for 25% of N turnover
• Controlling crop parasitic is £84bn industry – some driven by a demand for “perfect” food
• Potato cyst nematode, root knot nematode
• Also transfer of crop disease (tobacco rattle virus) or colour “break” in tulips
Nematodes
• Nematicides – kill ALL nematodes
• Only 15% of nemtodes in soil are plant parasites – the rest are largely beneficial or indifferent...
• Most nematode are in top 10cm of soil – nematostats to freeze or confuse nematodes while the roots get past.
Nematodes
• Successful body plan – colonise almost every habitat
• Ecdysozoa – closer to insects than worms
• Different sexes, hermaprodite and parthenogentic
• Long thin body gut, anus followed by tail
• Mouth has oesophogeal bulb – pumps in and out
• Stylet, mouth, head, body and tail shapes used in ID
• ~30 features to get to species level.
• However, quick and useful approach is to assign to trophic guilds (more later!)
Nematode sampling and extraction
• Sample in spring and autumn is usually the best time to sample – move up and down the soil profile (90cm) in response to drought
• Nematodes can have aggregated distributions in fields
• Soil samples from at least top 10cm, taken on W walk
• Store samples at 4oC – won’t breed, die or eat each other
• Bulk and mix samples
• Get 200g field-moist soil for extraction
Nematode sampling and extraction
• Baermann extract
• Funnel filled with water, tube attached to bottom
• Half submerged layer of soil on kleenex
• Nematodes wriggle through, fall down and get caught in bottom.
• 95% of nematodes are extracted
• Decant off water
• Kill in 60oC for 1 minute – attitudes on death can help!
• store in preservative – for long term gradually add glycerol to replace water
Nematode Trophic Guilds
• Soil nematodes feed on different things and are adapted to do so.
• Balance of different feeding groups can indicate structure of food web and longer term abundance of bacteria, fungi etc.
• 8 trophic groups identified, of which only 5 concern us.
• Plant parasitic
• Bacterivore
• Fungivore
• Omnivore
• Predatory
Plant parasites
• All have long thin stylets, usually with a pair of knobs
• CAN have long thin curved stylet with no knob though
• Slow moving (as is their food)
• Often annulated
“Bacterivores”
• No distinguishing features – “boring”
• Mouth is a funnel for hoovering up bacteria.
• Often small and fast moving
• Heat death posture is curved
• Some fungivores look like this...
“Fungivores”
• Fungal hyphae are noodles for nematodes
• They eat with chopsticks and elaborate forks!
• However, many sources describe these as being brushes for tidying up bacteria and describe fungivores as having stylets
• Some fungivores don’t have these.
• Roy Neilson calls elaborate mouthed, stylet-free nematodes fungivores – so we will too!
“Fungivores”
• Fungal hyphae are noodles for nematodes
• They eat with chopsticks - tentacles
• Some fungivores have stylets
Nematophagous fungi
• Fungi don’t seem to like nematodes!
– eat them from the inside
– trap them in nooses
– stun them with toxins
Omnivores
• Have short thick stylets with no knobs
• Stylet tip like an arrowhead
• Larger animals
• Not usually annulated
Predators
• Large creatures
• Big mouth cavities
• Normally with pointed teeth
• Sandworms of Dune!
Tardigrades
• “Slow walkers”
• First seen in the early days of microscopy
• “kleine wasserbär” – water bears
• AKA moss piglets
• Found in moss, also soil, freshwater and marine
• Marine look very strange – all paddles!
• 2 types of terrestrial
– Eutardigrades – chubby and plain
– Heterotardigrades – spiky and plated
• Ecdysozoa, oesohphageal bulb, stylet – but 8 legs (muscles are 1 cell!) with 2 pairs of claws
• Diagnostic feature is usually claw
Heterotardigrade
Tardigrades
Rotifers
– Wheel animals
– Only females!
– Also go into stasis, and take on genetic material from their food when they re-wet.
– Found in freshwater and soils – wide variety of body shapes and sizes
– Soil rotifers are often bdelloid – means leech-like
