Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture: A Guide

By Graham Stirling, Helen Hayden, Tony Pattison and Marcelle Stirling

Our capacity to maintain world food production depends heavily on the thin layer of soil covering the Earth's surface. The health of this soil determines whether crops can grow successfully, whether a farm business is profitable and whether an enterprise is sustainable in the long term. Farmers are generally aware of the physical and chemical factors that limit the productivity of their soils but often do not recognise that soil microbes and the soil fauna play a major role in achieving healthy soils and healthy crops.

Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture provides readily understandable information about the bacteria, fungi, nematodes and other soil organisms that not only harm food crops but also help them take up water and nutrients and protect them from root diseases. Complete with illustrations and practical case studies, it provides growers and their consultants with holistic solutions for building an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and suppressing root pests and pathogens.

The book is written by scientists with many years' experience developing sustainable crop production practices in the grains, vegetable, sugarcane, grazing and horticultural industries.

This book will be useful for: growers, consultants, agronomists and soil chemists, extension personnel working in the grains, livestock, sugarcane and horticultural industries, professionals running courses in soil health/biological farming, and students taking university courses in soil science, ecology, microbiology, plant pathology and other biological sciences.

• Language: English
• Publisher: CSIRO PUBLISHING
• Release date: Mar 1, 2016
• ISBN: 9781486303069

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© Graham Stirling, Helen Hayden, The State of Queensland through the Department of Agriculture and Fisheries (DAF) and Marcelle Stirling 2016

All rights reserved. Except under the conditions described in the Australian Copyright Act 1968 and subsequent amendments, no part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, duplicating or otherwise, without the prior permission of the copyright owner. Contact CSIRO Publishing for all permission requests.

National Library of Australia Cataloguing-in-Publication entry

Stirling, G. R. (Graham R.), author.

Soil health, soil biology, soilborne diseases and

sustainable agriculture : a guide /Graham Stirling,

Helen Hayden, Tony Pattison and Marcelle Stirling.

9781486303045 (paperback)

9781486303052 (epdf)

9781486303069 (epub)

Includes bibliographical references and index.

Soil ecology – Australia.

Soil biology – Australia.

Soilborne plant diseases – Australia.

Sustainable agriculture – Australia.

Hayden, H.L., author.

Pattison, Tony, author.

Stirling, Marcelle, author.

577.570994

Published by

CSIRO Publishing

Locked Bag 10

Clayton South VIC 3169

Australia

Telephone: [phone]

Email: [e-mail]

Website: www.publish.csiro.au

Front cover: (top) Canola-wheat rotation (Helen Hayden, Department of Economic Development, Jobs, Transport and Resources, Victoria); (middle) pathogen-affected roots (Tony Cooke, Department of Agriculture and Fisheries, Queensland); (bottom) cultivated soil (Helen Hayden, Department of Economic Development, Jobs, Transport and Resources, Victoria).

Back cover: (clockwise from top left) Mite (Gupta Vadakattu, CSIRO); feeding female root-knot nematode (Tony Cooke, Department of Agriculture and Fisheries, Queensland); bacteria decomposing residues from a cereal crop (Anthony Young, University of Southern Queensland); soil fungus (Marcelle Stirling, Biological Crop Protection Pty Ltd); bacterial wilt symptoms on tomatoes (Tony Pattison, Department of Agriculture and Fisheries, Queensland); earthworm (Graham Stirling, Biological Crop Protection Pty Ltd); electron micrograph of fungi binding plant residues to soil particles (Gupta Vadakattu, CSIRO); root-lesion nematode (Pratylenchus thornei) (Kirsty Owen, University of South Queensland).

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Contents

Preface

Acknowledgements

Acknowledgements for figures, and copyright issues

About the authors

Chapter 1 Introduction: soil health, soil biology, sustainable agriculture and evidence-based information

What is soil health?

What is sustainable agriculture?

Soil health and sustainable agriculture are inextricably linked

The role of soil organisms

The need for holistic solutions to soil-health problems

Why is evidence-based information important?

Outline of the book, and its purpose

Chapter 2 Soil physical, chemical and biological properties, and the key role of organic matter in promoting soil and plant health

Soil composition

Mineral particles

Air

Water

Organic matter

Soil properties

Soil physical properties

Soil chemical properties

Soil biological properties

The key role of organic matter in modifying soil properties and improving soil health

Organic matter and soil physical health

Organic matter and soil chemical health

Organic matter and soil biological health

Common soil physical and chemical constraints

Concluding remarks

Chapter 3 Organisms in the soil food web and their functions

Soil biodiversity

Bacteria

Fungi

Archaea

Cyanobacteria and algae

Protozoa

Nematodes

Mites and collembolans

Enchytraeids, symphylans, tardigrades and other mesofauna

The macrofauna: millipedes, centipedes, spiders, termites, ants, scorpions and earthworms

The soil food web

Interactions between organisms in the soil food web

Ecosystem services provided by the soil biota

Improvement of soil structure and soil water regimes

Production, storage and release of nutrients

Suppression of soilborne pests and pathogens

Plant growth promotion

Degradation of toxic compounds

The soil–root interface: a key site of biological activity

Maintenance of the energy sources required to sustain soil biological processes

Concluding remarks

Chapter 4 Soilborne diseases: a major impediment to crop production

Diseases caused by Rhizoctonia

Root rot, crown rot and vascular wilt diseases caused by Fusarium

Take-all of cereals caused by Gaeumannomyces graminis

Root rot and damping-off diseases caused by Pythium and Phytophthora

Pachymetra root rot of sugarcane

Diseases caused by Sclerotinia and Sclerotium

Bacterial wilt caused by Ralstonia solanacearum

Crown gall

Diseases caused by nematode pests

Sedentary endoparasites

Migratory endoparasites

Ectoparasites

Estimating the amount of pathogen inoculum in soil

Effects of environment and management on pathogen inoculum levels and disease severity

Diagnosis of soilborne diseases

Integrated disease management

Chapter 5 Impact of natural enemies on soilborne pathogens

Interactions within the soil food web and their effects on soilborne pests and pathogens

Classical, inundative, and conservation biological control, and its relevance to soilborne pests and pathogens

Disease-suppressive soils: organic matter-mediated and specific forms of suppression

Benefits and limitations of different forms of suppression

Identification of disease-suppressive soils, and indicators of suppression

Impact of management on disease suppression

The key role of organic matter in improving soil health and enhancing disease suppression

Examples of disease suppression

Biological suppression of Rhizoctonia root rot

Take-all decline of cereals

Disease suppression in horticulture

Specific suppression of plant-parasitic nematodes

The role of organic and biological products in improving plant growth or enhancing disease suppression

Soil improvers, bio-stimulants and plant-growth promoters

Bio-inoculants

Biopesticides

Confirming the efficacy of organic and biological products

Concluding remarks

Chapter 6 A practical guide to improving soil health and reducing losses from soilborne diseases

Assess soil health and identify any physical, chemical and biological constraints

Soil physical and chemical factors

Soilborne diseases

Low biological activity and diversity

Determine the main limiting factors

Identify options for improvement

Monitor soilborne pathogens and beneficial organisms

Modify soil and crop management practices

Instigate a continuous process of assessment, modification and re-assessment

Concluding remarks

Case study: Growers and consultants use a root disease testing service to monitor pathogens and reduce losses from soilborne diseases

Chapter 7 Grain farming systems to improve soil health and enhance biological suppression of soilborne diseases

Conservation agriculture: the first step in building an active, diverse and resilient soil biological community

Conservation agriculture and soil organic matter

The key role of high cropping intensities and crop rotation

The biological impact of conservation agriculture

Second-tier practices to continue the soil improvement process

Avoidance of compaction through traffic control

Biomass-producing cover crops and organic amendments

Integrated crop and livestock production

Site-specific management of inputs

Integrated pest management systems

Options to further improve best-practice farming systems

More effective plant nutrition

Greater levels of disease suppression and biological control

Improved resilience under stress

Concluding remarks

Case study: Reducing risk in a drought-prone environment by improving nutrient use efficiency

Chapter 8 Annual and perennial pastures to improve soil health in grain-cropping systems

The role of perennial pastures in improving soil health

The impact of climate and pasture species on soil biological properties

The contribution of mixed farming systems to sustainability

Choice of pasture species

Options for the future

Concluding remarks

Case study: Living roots mean a healthy, living soil

Chapter 9 Yield decline of sugarcane: a soil health problem overcome by modifying the farming system

The conventional sugarcane farming system

The impact of the conventional sugarcane farming system on soil health

Soil structure/compaction

Pests and pathogens

Soil organic matter

A more sustainable sugarcane farming system

Soil health and biological benefits from the new farming system

The impact of the new sugarcane farming system on soilborne pests and pathogens

Effects on Pachymetra root rot

Managing nematode pests with rotation crops

The impact of tillage on the resurgence of nematode pests

Enhancing suppression of nematode pests with inputs of organic matter

Specific suppression of nematode pests by bacteria in the genus Pasteuria

Effects of pesticides and fertilisers on the biological health of sugarcane soils

Improving soil health is a long-term process

Concluding remarks

Case study: Incremental changes to a sugarcane farming system improve soil health and profitability

Case study: Controlled traffic and soybean rotation crops produce multiple benefits in a sugarcane farming system

Chapter 10 Vegetable farming systems: the challenge of improving soil health and sustainability in an industry that demands high levels of productivity

High-input vegetable production systems

Possible components of more sustainable vegetable production systems

Crop rotation, cover crops, companion planting and residue retention

Biofumigation

Appropriate planting times and cultural practices

Reduced tillage

Controlled traffic

Precision agriculture

Organic amendments

Nutrient management

Irrigation management

Integrated management of pests and diseases

Organic and biological products

Organic production

Integrated management systems

Concluding remarks

Case study: No-till zucchini production reduces costs and improves soil health in the dry tropics

Case study: Sustainable vegetable production on land prone to soil erosion

Chapter 11 Options for improving soil health and minimising losses from soilborne diseases in perennial horticultural crops

Reducing or eliminating tillage

Using cover crops to maintain ground cover

Minimising compaction

Mulching

Organic amendments

Examples of disease management systems for perennial crops

The Ashburner system of controlling Phytophthora root rot of avocado

Mulching to reduce specific replant disease in apple orchards

Root disease management in banana

Enhancing specific agents to suppress particular pathogens

Concluding remarks

Case study: Managing soil, water and nematode pests on a banana plantation in a tropical environment

Case study: Wine-grape production with a focus on sustainability

Chapter 12 Key soil health messages, and practices that should be included in holistic soil improvement programs

The main messages from the book

Key practices to improve soil health and sustainability

References and further reading

Index

Preface

Anyone involved in agriculture will recognise that soil is one of their most important assets. A soil may not be highly fertile and may vary in composition across the farm, but, together with water, it is the resource that determines whether crops can be grown successfully, whether a farm business is profitable, and whether an enterprise is sustainable in the long term.

Farmers are generally aware of the soil physical and chemical constraints that limit the productive capacity of their soils. They see problems such as compaction, waterlogging, hard-setting, surface-sealing and poor water-holding capacity when they drive around the farm or plant their crops. They know that high acidity or excessive salinity will reduce crop yields, and they have to cope with issues such as phosphorus fixation and low nutrient retention when deciding how to fertilise their crops. Thus, it is not surprising that most of the soil-health literature available to farmers focuses on identifying the physical and chemical constraints that limit plant growth.

When dealing with soil-health problems, farmers tend to forget, or may not even be aware, that soil has a biological component. Most will know something about the fungi, bacteria and nematodes that cause root diseases, because they are found in all agricultural soils, and can markedly reduce crop yields. However, they probably know very little about the beneficial organisms that play an important role in maintaining soil structure, fixing nitrogen from the atmosphere, storing and cycling nutrients, and protecting plants from soilborne pests and pathogens.

This book takes a holistic view of soil, but focuses on the biological component. It not only discusses the soilborne pests and pathogens that debilitate the root systems of all crop plants, but also covers the multitude of microbes and small animals that improve soil fertility, enhance plant growth and suppress disease. It argues that beneficial organisms have an important role to play in soil, and demonstrates that soil physical and chemical fertility can be improved, and losses from soilborne diseases reduced, when steps are taken to enhance biological activity and diversity.

The challenge in writing this book was to provide a reasonably complete, but relatively simple, coverage of a multi-faceted topic. Soils contain a myriad of bacteria and fungi, enormous numbers of other microscopic organisms and a wide range of larger animals such as insects and earthworms. This means that soil is the most complex ecosystem on Earth. Not only are there enormous numbers of species, but the population densities of individual species constantly change in response to the presence of food sources such as roots and plant residues, and to competition from other members of the soil biological community. To add to this complexity, all soil organisms are affected by environmental factors such as moisture and temperature, by the physical and chemical properties of the soil, and by a range of agricultural management practices. Thus, this book should be seen as no more than a brief introduction to a topic that scientists are still struggling to fully understand.

As a group of authors, we have many years experience working with fungi, bacteria, nematodes and microarthropods. Thus, we have a reasonably good understanding of how soils function. Our aim has been to amalgamate that knowledge into a form that is useful to readers who may have never looked down a microscope or considered soil from a biological perspective. Despite the complexities of soil, we have tried to keep the message simple. Instead of providing an in-depth coverage of the vast array of organisms that live in soil, we have focused on the steps farmers can take to increase soil biological activity, enhance biodiversity and improve the health of their soils.

Our main target audience is Australian farmers. However, they live in widely different environments, grow a variety of crops, and have a diverse range of production goals. In an attempt to make the book relevant to everyone, chapters specific to different types of agriculture (broadacre grain crops, vegetables, sugarcane, pastures and perennial horticulture) have been included. Although some readers may consider that these chapters are not relevant to their production system, we would encourage them to learn how growers in other industries are dealing with their soil-health problems. A practice being used in one industry may be worth trying in a quite different form of agriculture.

Another group that we hope will find this book useful are the consultants who provide advice and technical support to farm businesses. Many of these professionals will have taken courses in soil physics and chemistry at a tertiary institution, but may have only a cursory knowledge of soil biology and plant pathology. Hopefully the book will enable them to communicate more effectively with their clients in areas such as soil health, plant nutrition and soilborne disease management.

We also hope that the next generation of agriculture students will read our book and reflect on its key messages. They will have to face many different soil-health problems during their working lives, and it is important that they understand how soils function from a biological perspective.

Although Australian farmers and their consultants are the primary targets of this book, we hope that it will also be useful to land managers in other countries. Australia has some of the poorest soils and one of the most variable climates in the world, but an emphasis on research, together with a culture of innovation within the farming community, has put it in good position to overcome its soil-health problems. Most of the steps that are being taken to improve Australian soils will be applicable in other countries.

We accept that many people in our target audience will find this book too complex, or will argue that it lacks specific recommendations that can immediately be adopted. Most farmers expect scientists to undertake research and then develop simple management recommendations that can be passed on to them by local extension personnel. That approach works well when dealing with relatively simple issues such as determining fertiliser or pesticide inputs, but is not appropriate when ecologically based soil management systems are being considered.

If farmers are to improve the health of their soils and make their farming systems more sustainable, they must be able to manipulate the myriad of biotic interactions that occur in soil. Since that requires some understanding of soil ecological processes, we do not apologise for the book’s complexity. And the reason we have avoided making specific recommendations is that in real farming systems, multiple variables act in site-specific ways. Thus, we have emphasised the need for farm-based field trials, because they are the only way of deciding which practices are likely to be effective in the local production system, soil type and environment.

We have enjoyed working together to write this book and hope that it will encourage farmers to take up the twin challenges of improving the health of their soils and making their farming system more sustainable.

Graham Stirling, Helen Hayden, Tony Pattison and Marcelle Stirling

April 2015

Use of information in this book

In preparing this book, the authors’ intention was to provide the reader with a broad overview of soil biological processes and their role in influencing soil and plant health. Since the activity of soilborne pests and pathogens and the beneficial organisms that coexist with them is influenced by soil type, environment, the principal crop and many other factors, the material contained in the book is general and not meant to be prescriptive. The reader/user should obtain expert advice as to whether the guidelines and management practices discussed in this book are effective or appropriate in a particular location, farming system or environment. Results from local and on-farm field trials, together with extension material relevant to the local region, should always be used as a basis for decision making.

Acknowledgements

This book could not have been written without the help of many people, though Ken Pegg (Department of Agriculture and Fisheries, Queensland), Daniel Huberli (Department of Agriculture and Food, Western Australia), Phil Moody (Department of Science, Information Technology and Innovation, Queensland), Peter Sale (La Trobe University) and Alan McKay (South Australian Research and Development Institute) deserve a special mention. They acted as referees and made many useful comments on an early draft of the book. Although we take total responsibility for the final version, their contributions are very much appreciated.

Many other people helped by providing information or responding to our queries, and we would like to thank them sincerely. They included Steven Simpfendorfer, Mike Bell, Nikki Seymour, Alan Garside, Michael Rettke, Jacky Edwards, Gupta Vadakattu, Joanna Petkowski, Pauline Mele, Merran Neilsen, Elio Jovicich and Paul O’Hare.

Since our book focuses on the practices farmers can use to restore the health of their soils, we felt it was important to demonstrate that, with planning and persistence, it is possible to overcome soil-related constraints that are limiting productivity. Eight case studies have been included and the farmers who contributed deserve our special thanks. Allen Buckley, Stuart McAlpine, Tony Chapman, Ashley Petersen, Paul Le Feurve, Bob and Beth Euston, Craig Buchanan and Robin Nettelbeck all took time out of their busy schedules to talk to us, and were willing to explain the benefits that can be obtained when soil-management practices are improved. Their stories cover many of the issues farmers have to face when trying to improve the condition of their soils, and the knowledge they gained during the process will be invaluable to others.

Shawn Rowe helped us prepare a ninth case study on SARDI’s root disease testing service, and we thank him sincerely for his help. However, the detail in that case study could not have been presented without contributions from several consultants who were using PreDicta B™ (Drew Penberthy, James Miller, Simon Mock, Chris Pearce and David Cameron) and some of the farmers who were benefiting from the results (Alwyn Dwyer, Mark Siviour and Jim Hamilton). Because they were willing to tell us what they had learnt from using the service, we were able to demonstrate that monitoring pathogens is a worthwhile exercise in all of Australia’s grain-growing regions.

One person we are particularly grateful to is Martin Barry from Brisbane Digital Images. He scanned many of our images and prepared some of the figures, and his professionalism and attention to detail enabled us to focus on other aspects of the book.

Although they were not directly associated with the book, we would like to thank the funding bodies that have supported our research programs over many years. They cover the wide spectrum of Australian agriculture and without their support we would not have had the knowledge required to write a book of this nature. The Grains Research and Development Corporation (GRDC) has been a key contributor, as it has funded two major research programs in soil biology over the last 15 years (Soil Biology Initiatives I and II), and contributed to the development of the root disease testing service discussed in Chapter 6. We, together with many other scientists, have also received support from Sugar Research Australia (SRA – formerly the Sugar Research and Development Corporation), Horticulture Innovation Australia (HIA – formerly Horticulture Australia Limited), Meat and Livestock Australia (MLA), Rural Industries Research and Development Corporation (RIRDC) and Australian Centre for International Agricultural Research (ACIAR).

The support of our employers is also acknowledged, as they have provided the resources we required to undertake this task. Graham and Marcelle Stirling are directors of their own company (Biological Crop Protection Pty Ltd); Helen Hayden is employed by the Department of Economic Development, Jobs, Transport and Resources in Victoria; and Tony Pattison is based in north Queensland with the Department of Agriculture and Fisheries.

Writing a book involves many solitary hours in front of a computer, and so it impacts on family and friends. Graham and Marcelle coped by working on the book together, but Helen would like to thank Trevor Perry, and Tony his wife Sue, as their support was invaluable when they were in writing mode.

Finally, we wish to acknowledge the contributions of our colleagues in many fields of agriculture, whose research over many years has provided us with a better understanding of how soils function. The challenge of the future is to use that knowledge to improve the way we manage our agricultural soils.

Acknowledgements for figures, and copyright issues

Many colleagues and organisations have provided photographs and diagrams to illustrate this book, and we gratefully acknowledge their input. All contributions, together with the relevant figure number, are listed below. Photographs used in case studies are also included, but are designated by the page on which they are found.

Please note that the copyright for these images is held either by the organisations listed, or the person who contributed the material, and remains their property. The designated contributor (organisation or person) must be contacted for permission to use any photograph, diagram or figure in this book.

Department of Agriculture and Fisheries, Queensland

From various publications: 2.7; 3.16; 4.6B; 4.14B; 4,15A; 4.15B, 4.16B; 4.17; 4.18; 4.21; 4.22A; 4.22B; 4.25; 4.26A; 4.27; 10.3A; 10.3B; 10.3C; 10.3D; 10.3E; 11.5A.

Tony Pattison: 1.1A; 1.1B; 2.1; 2.4; 2.5; 2.6; 2.8; 2.9; 2.10A; 2.10B; 3.8A; 3.8C; 3.8E; 4.6A; 4.16A; 4.26B; 5.9A; 5.11A; 5.12; 6.3A; 6.3B; 10.6A; 10.7; 10.8B; 10.10A; 10.10B; 10.10C; 10.10D; 10.10E; 10.10F; 11.2; 11.3A; 11.4A; 11.4B; Case study images on pp. 206 and 226.

Tony Cooke: 4.1B; 4.9A; 4.9B; 4.12; 4.19A; 4.19B; 4.19C; 4.20C; 11.5B; 11.6.

Nikki Seymour: 3.14.

Ian Layden: 6.6.

Merran Neilsen: 11.7.

Department of Economic Development, Jobs, Transport and Resources, Victoria

Helen Hayden: 3.4; 4.3A; 4.3C; 5.8; 5.14; 6.5A; 6.5B; 7.1A; 7.1B; 7.2A; 7.2B; 7.2C; 11.3C.

Tonya Wiechel: 4.1A.

Fran Richardson: 4.4.

Grant Hollaway: 4.7A; 4.7B.

Biological Crop Protection Pty Ltd

Marcelle Stirling: 1.2; 2.2; 2.3; 3.1; 3.3A; 3.5; 3.9; 3.11; 3.15; 3.20; 4.5; 5.1; 5.2; 5.3; 5.5; 5.6; 5.7; 5.10; 5.17.

Marcelle Stirling (images included in Stirling (2014) published by CABI): 3.6; 3.17; 3.19.

Graham Stirling: 3.7; 3.10; 3.12; 3.13; 3.18; 3.21; 4.10; 4.11A; 4.11B; 4.14A; 4,20A; 4.20B; 4.28A; 4.28B; 4.29; 5.4A; 5.4B; 5.4C; 5.4E; 5.4F; 5.9B; 5.11B; 5.16; 6.1; 6.2; 6.4; 6.7; 9.11; 9.13; 9.14A; 9.14B; 9.15; 10.1A; 10.1C; 10.1D; 10.1E; 10.2; 10.4A; 10.4B; 10.5A; 10.5B; 10.5C; 10.6B; 10.9A; 10.9B; 10.9C; 11.3B; 11.8; 11.9A; 11.9B; 11.10; Case study images on pp. 183 and 184; images A and C on p. 164.

South Australian Research and Development Institute

Alan McKay: 4.2A.

Paul Bogacki: 4.2B.

Margaret Evans: Case study image on p. 135.

Department of Agriculture and Food, Western Australia

Sarah Collins: 4.8A.

Ktihsiri Jayasena: 4.8B.

CSIRO

Gupta Vadakattu: 3.2B; 3.3B; 3.8B; 3.8D; 5.13; 5.15.

James Hunt: 7.3.

Bill Davoren: Case study image B on p. 164.

CSIRO Science Image

8.1A; 8.1B; 8.1C.

University of the Sunshine Coast

David Walter: 5.4D.

University of South Australia

Jack Desbiolles: 4.3B.

University of Southern Queensland

Anthony Young: 3.2A.

Kirsty Owen: 4.23A; 4.24A; 4.24B.

John Thompson: 4.23B.

Sugar Yield Decline Joint Venture

Alan Garside: 9.1; 9.2A; 9.2B; 9.3; 9.4B; 9.4C; 9.5; 9.6A; 9.6B; 9.6C; 9.6D; 9.6E; 9.6F; 9.6G; 9.6H; 9.6I; 9.6J; 9.7; 9.8; 9.9; 9.10; 9.12.

Sugar Research Australia

Barry Croft: 4.13A; 9.4A.

Rob Magarey: 4.13B.

Orchard Services Pty Ltd

Stephen Tancred: 11.1A; 11.1B.

Victorian Strawberry Industry Certification Authority

Scott Mattner: 10.1B.

McAlpine Farms

Stuart McAlpine: Case study images on p. 153.

The Euston family

Bob Euston: 10.8A; Case study images on p. 209.

Agronomo

Andrew Storrie: 8.2.

Paul Jones Photography

Paul Jones: 8.3.

Yalumba

Darrell Kruger: Case study image A on p. 229.

Robin Nettelbeck: Case study image B on p. 229.

About the authors

Dr Graham Stirling is a plant pathologist/nematologist/soil ecologist in a company that provides research and disease diagnostic services to Australia’s rural industries. In a career spanning 45 years, he has worked on many of the crops grown in Australia, including cereals, lucerne, rice, various pasture species, sugarcane, grapes, stonefruit, apples, citrus, pineapples, turfgrass, tomatoes, potatoes, capsicum and ginger.

Graham began his career in the South Australian Department of Agriculture, where he played a key role in introducing nematode-resistant rootstocks to the wine grape industry. He then joined the Queensland Department of Primary Industries and began working with tropical and subtropical crops. In 1997, he and his wife Marcelle established their own business, and since then have jointly undertaken research on soilborne-disease problems in a wide range of crops.

Graham has always had an interest in beneficial soil organisms, and his books on biological control of plant-parasitic nematodes are widely used as sources of information on sustainable methods of managing nematode pests. He has also published more than 100 peer-reviewed papers. In recent years, his research has been aimed at improving our understanding of nematode-suppressive soils, and developing indicators that can be used to assess the biological status of agricultural soils.

Dr Helen Hayden is a soil microbial ecologist at the Department of Economic Development, Jobs, Transport and Resources in Victoria. Helen started her career as a plant pathologist over 23 years ago, learning many practical skills while working at the Queensland Department of Primary Industries. She completed her PhD at the University of Queensland in 2000, specialising in diseases of bananas. Moving south to work at the University of Melbourne, Helen shifted focus to the grains industry, in particular blackleg disease of canola. Since 2006 she has worked for the Victorian Government researching soil microbiology using new technologies to advance the study of microbes in Australian soils.

Helen has investigated the soil microbial communities and functions of dairy soils, grain cropping systems, remnant ecosystems and the effects of elevated CO2 and temperature on a native pasture. Helen’s recent research in disease suppressive soils for Rhizoctonia in cereals has brought together her two interests of plant pathology and microbial ecology, and inspired her contribution to this book. Helen’s interest in microbial ecology comes from the fact that microbes are everywhere and with new technologies and interdisciplinary approaches we can start to identify ‘who is there’ and ‘what they’re doing’. In the case of soil, the key to interpreting this information always lies in knowledge of the site, soil characteristics, land-use history and environmental conditions.

Dr Tony Pattison is the Principal Nematologist and Soil Health team leader for horticulture within the Queensland Department of Agriculture and Fisheries. Tony started his career working on cotton and wheat in north-west New South Wales, but for the past 21 years has been based at the Centre for Wet Tropics Agriculture at South Johnstone in north Queensland. Tony’s role has been to investigate plant-parasitic nematodes and soil-health-related issues in a diverse range of tropical horticultural crops including banana, mango, papaya, avocado, ginger and annual vegetables. His work with bananas has resulted in the industry being able to divorce itself from chemical nematicides and move to safer and more effective alternatives.

Tony has the viewpoint that to improve agricultural sustainability it is better to understand why a problem has occurred and then fix the causes, rather than just treat the symptoms. This has led to close collaborations with primary producers, ensuring a mutual exchange of information and the development of practical solutions to soil-based problems. It has also led to international collaborations in Central America, the Pacific Islands, Indonesia and the Philippines. Tony’s interest in soil ecology and disease suppression currently focuses on competition for carbon within the soil.

Dr Marcelle Stirling is a plant pathologist/microbiologist who has worked on many aspects of soil biology. Her research career began at the University of California, Riverside in 1975, where she studied nematode-trapping fungi. She also worked on nematodes that were being used as biocontrol agents for mosquitoes, and helped develop control measures for a fungal parasite that was preventing the successful culture of the nematode.

After returning to South Australia, Marcelle was involved in a research project on fungal parasites of cereal cyst nematode. A move to Brisbane in 1983 gave her the opportunity to work on a wider range of fungi, and also help postgraduate students at the University of Queensland with fungal identification and plant pathological techniques. Later, she contributed to a research project on biological control of Rhizoctonia and Pythium in cotton seedlings, and also studied the role of microorganisms in suppressing an important pathogen of avocado fruit.

Since 1997, Marcelle has completed research projects on Fusarium rhizome rot of ginger, Phytophthora root rot of pineapples, and die-back in golf greens caused by ectotrophic root-infecting fungi. She has also operated a plant disease diagnostic clinic and is one of the few scientists in Australia able to identify the wide range of free-living nematodes found in Australian agricultural soils.

Chapter 1

Introduction: soil health, soil biology, sustainable agriculture and evidence-based information

Our capacity to maintain