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 organisms • Get to know a range of water-dwelling soil organisms • Be able to identify functional feeding groups (trophic guilds) • Understand anatomy and ecology. • Be able to identify springtails to species. • Understanding 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: 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 , 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

• What is soil? • Soil organisms – a tour • What soil life does for us • What we do to soil life • Conservation of soil biodiversity – the beginning...

Photos: M Shepherd

Image: reconstructionDrawings: Aberdeen of first Universityland plants after in ordovician,Scourfield (1940a, Jose Bonner b) and HirstCC BY 1923-SA 3.0 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 Biomass and numbers

In a handful of soil...

HEXAPODS

Image: Karl Ritz, Cranfield University Photo: Matthew Shepherd Photo: Matthew Shepherd Types of Soil Organisms

• 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 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, , ... • 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... Myxobacteria photo: Michiel Vos doi:10.1371/journal.pbio.0030398 Photo: GrahamColm at en.wikipedia

Bacteria

Photo: Julia Plotnikov

Bacteria & Archaea • Tiny chemical engineers • Rapid reproduction - can make use of sudden resource availability • Dormancy • Form biofilms • Hate fungi • Team up with plants

Firmicutes Photo: Wikimedia commons Photo: Matthew Shepherd

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... 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 And the rest... Symphyla

Flies Thrips Photo: Michel Vuijlsteke

Bristletails (diplura) Coneheads () Pauropods

Beetles

Booklice (psocids) Pseudoscorpions

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 • Most soils wouldn’t have structure without soil life • How? Like a morning in a playgroup!

Moving Painting

Photo: Matthew Shepherd

Gluing Eating Sewing Image: Karl Ritz, Cranfield University

Photo: Matthew Shepherd

Photo: Joseph Morton, West Virginia University 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? CO2

CO2

CO2

Decomposition… … 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

Nutrient Release C N

C N

C N

C N

C N C N 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! Painting Moving

Gluing Eating Sewing 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

… and what we do to the soil biota...

• 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!

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 Soil organic matter and total soil PLFAs

1800 y = 395.32ln(x) - 491.93

1 R² = 0.8434

- 1600 1400 1200 1000 800 600 400

Total Soil PLFA content nmg content PLFA Soil Total 200 0 0 20 40 60 80 100 % Soil Organic Matter (Loss on Ignition)

Source: Natural England, ECBN data, 2011-2013 Soil organic matter = better soil structure Grassland soil organic carbon and bulk density in England and Wales

1.80 y = -0.433ln(x) + 1.5756 1.60 R² = 0.5348

1.40

1.20 1.00 0.80

0.60 Bulk density density Bulkg/cm 0.40 0.20 0.00 0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00 % organic carbon (Walkley-black)

Source: ADAS, Defra project BD5001 Soil organic matter = better drought resistance GB soil organic matter and soil moisture content 120 y = 21.517ln(x) - 12.746 R² = 0.8866

100

80

60

40

20 % Soil water content water Soil %

0 0 20 40 60 80 100 -20 % Soil Organic Matter

Source: Countryside Survey, 2007 Soil organic matter = better nutrient retention

Soil organic matter and cation exchange capacity 140 y = 30.422ln(x) - 37.506 R² = 0.6967 120Big improvements 100 in80 soil function due

60 100g_1 40to small increases 20

Cation Exchange Capactity (mEq (mEq Capactity Exchange Cation 0 0 from20 40low 60 SOM80 100 % Soil organic matter (loss on ignition)

Source: Countryside Survey, 2007 Soil organic matter

• Raise organic matter - put more in, or lose less • Add more organic matter from elsewhere • Grow more plants!

Looking after life in the soil • 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 Conservation of Soil Biodiversity • 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 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?

Conservation of Soil Biodiversity Conservation of Soil Biodiversity • Soil fauna monitoring data sparse • Even common species look rare! 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?

Improving knowledge & Recording

• 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?

Facebook Group https://www.facebook.com/#!/groups/438740999565613/ 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 Nematodes and Soil Water Fauna

• 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

Protists • 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.

Protozoa • 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

Testate Amoeba

Cercozoa

Slime Moulds

https://www.youtube.c om/watch?v=BZUQQmc R5-g https://www.youtube.c om/watch?v=5h8WOW EqP6o

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 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