Red flag over deteriorating health of forest soils

Planting successive rotations of the same tree species on the same piece of land over and over is likely to have a negative impact on soil health and long term productivity of the site will decline – especially when the residue from the previous harvest has been burnt off, leaving the soil unprotected from the elements, as is the case with this community forestry enterprise in Eastern Cape.

Planting the same tree species over successive rotations carries a high risk of deteriorating soil health, say FABI researchers …

It is widely accepted in agriculture circles that practicing crop rotation is beneficial for soil health. This is because the continuous cultivation of the same plant species on the same piece of land over and over again impacts negatively on soil health, and leads to a build-up of harmful micro-organisms. There is plenty of scientific evidence to support this theory.

To address this issue, good farmers all over the world practice crop rotation, planting different crops over successive rotations, or do inter-cropping where for instance they will plant a legume in between rotations to improve soil health and biodiversity.

Many small-scale tree farmers in Zululand practice inter-cropping, planting mielies, beans or peanuts in between their Eucalyptus seedlings when they are still small, and before the canopy closes. This could be beneficial for soil health.

So why not treat short rotation tree crops the same way – and if we don’t, and we keep on planting the same species rotation after rotation, will we eventually find that soil health deteriorates to the point where the trees will no longer grow properly?

Common sense would suggest that this will be the case, but there is no ‘conclusive’ scientific evidence to support this theory. In any event crop rotation in forestry is not so easily done as rotation lengths are long (8 – 20 years), land available for forestry is limited (in South Africa) and only three species are widely grown – eucalypts, pine and wattle – all of which are geared to serve specific markets.

Moreover improvements in silvicultural practices and advances in tree breeding have thus far masked any impacts of deteriorating soil health on successive tree crops, thus reducing growers’ appetite for experimenting with crop rotation...

This Sappi compartment in Zululand has been mulched and the residue retained to cover the soil with a nutrient-rich layer that provides protection, retains moisture and gives the young trees a growth boost.

But now a group of highly regarded researchers have raised a red flag and warned that deteriorating soil health is a real risk for short rotation plantation forestry, as it is practiced in South Africa and in many other parts of the world.

A team of FABI researchers including Dr Tanay Bose, Prof Bernard Slippers, Almuth Hammerbacher, Jolanda Roux and Mike Wingfield, have analysed existing data on soil microbiomes from short-rotation forestry environments around the world which, they say, provides evidence that a build-up of harmful micro-organisms, depletion of beneficial micro-organisms, and deterioration of the physical and chemical properties of soil can result from continuous replanting of the same tree species on the same piece of land.

“Populations of unfavourable microbes can be expected to become more abundant over successive rotations,” state the FABI researchers in an article published in the journal Current Forestry Reports. “This is strongly supported by data from recent soil microbiome studies involving commercially managed forests, which provide convincing evidence of an increase in pathogenic microbes in soils of continuously replanted forests.”

Building on these findings and considering similar approaches in agriculture, the team proposes a number of practical solutions that have the potential to mitigate the deterioration of soil health resulting from planting the same species over successive rotations.

Weza farmer Jon Mackenzie uses a tractor-powered chipping machine to chip the post-harvest residue after clear felling, which is then spread evenly over the site before the re-planting operation begins. This is his strategy to conserve the health of the soil on his farm for the log term.

• Retaining post-harvest residue on the site is likely to result in healthier soils over successive rotations. This is why many growers have stopped burning the post-harvest residues and have opted for mulching or chipping.
• Application of biochar has considerable potential to enhance soil properties, nutrients and microbes in continuously replanted forests. Biochar is a carbon-rich, stable organic product made from the pyrolysis of organic biomasses such as leaves, sawdust, animal dung and wood. During carbonization, biochar releases phosphate into the soil along with other mineral nutrients, improving its fertility. Biochar also improves the physical properties and microbial biodiversity of the soil, which could further increase soil nutrient availability and carbon storage. However more research is needed to assess the impact of biochar on plantation soils.
• Crop rotation and intercropping could alleviate the negative consequences of continuous replanting of the same species in short-rotation plantation forestry. For example, rotating between eucalypts, black wattle and pine species could prevent the accumulation of harmful soil microbes detrimental to these trees. Rotating nitrogen fixing leguminous tree species such as Acacia with eucalypts or pines has the potential to further promote both soil and tree health increasing the availability of nitrogen in the soil and improving the quality of plant litter.
• Practicing agro-forestry, where different crops are inter-planted on the same piece of land, would also have a positive impact on soil health.
• Innoculation of tree seedlings in the nursery with beneficial microbes.
“Continuous replanting practised in short-rotation plantation forests is likely to be accompanied by a high risk of ‘replanting syndrome’ in plantations. While long-term monitoring programs to document the changes in soil microbiomes are still lacking and should be urgently initiated, the available evidence suggests that short-rotation forest plantation enterprises could be restrictive when successively establishing plots with the same or nearly the same genotypes,” the FABI team concluded.

Mulching after clear felling is an expensive exercise, but many growers have opted for this approach instead of burning off post-harvest residues, in the interests of boosting soil health for the long term.

For the full Report see: Current Forestry Reports.

Cypress canker threatens exotic & native trees in SA

Sick cypress trees in Welkom, Free State. Scientists from Fabi fear that this disease could have serious impacts on native cedar trees in South Africa.

Cypress canker is killing exotic cypress trees in South Africa and poses a serious threat to native cedars, setting alarm bells ringing among members of the scientific community …

Welkom, the second-largest city in the Free State province of South Africa, is often referred to as a ‘city within a garden’ thanks to its numerous parks and trees. Unfortunately, many of these trees are dying from a disease known as ‘Cypress canker’.

Italian cypress (Cupressus sempervirens) is a popular ornamental tree that has been widely planted in Welkom, and is found on traffic circles, in parks, private gardens and along entire avenues in several neighbourhoods. Italian cypress is, however, also particularly susceptible to cypress canker.

The disease is caused by a number of fungal species in the Xylariales and specifically in the genus Seiridium. Symptoms include bleeding cankers that deform stems and cut off the water supply above the canker. As a result, diseased trees show typical “flagging” symptoms resulting in the death of affected branches.

Dr Janneke Aylward, a Research Fellow at the Forestry & Agricultural Biotechnology Institute (Fabi) based at the University of Pretoria, recently visited Welkom as part of a project to investigate the cause of cypress canker in South Africa. This project was prompted by the recent discovery of cypress canker on native Widdringtonia nodiflora cedar trees in South Africa, which poses a real threat to native cedar species.

During her visit Janneke, assisted by staff of the Matjhabeng Local Municipality’s Department of Parks, Sports and Recreation, took samples of diseased cypress trees at 11 sites across Welkom. She will isolate the canker fungus present in the diseased branches and investigate their identity and diversity.

Fabi research scientist Janneke Aylward … on the trail of Cypress canker in a bid to better understand the fungus pathogen that also poses a serious threat to native cedar trees in South Africa.

Native cedars at risk

According to Janneke, the presence of cypress canker in one of our native cedars - the Mountain cedar Widdringtonia nodiflora – has set the alarm bells ringing in scientific circles. The disease was recently identified in Mountain cedar at one site in Franschoek. To date the disease has not been found on Widdringtonia wallichi (Clanwilliam cedar) in the Cederberg, and the Fabi team has not yet visited the Baviaanskloof in the Eastern Cape to look for the presence of cypress canker in Widdringtonia schwarzii (the Willowmore cedar).

The Clanwilliam cedar is critically endangered and the Willowmore cedar is near threatened, according to IUCN. Janneke believes that these two cedars are only found in a very specific range, so the chances are good that they have had little or no contact with other cedars that may carry the disease.

Janneke believes that the Mountain cedar will survive the canker because it's a species that re-sprouts after fire. When the fynbos vegetation burns, the pathogen should be destroyed and the infected trees will likely re-emerge. The other two native cedars, the Clanwilliam cedar and Willowmore cedar, do not re-sprout so cypress canker - combined with the fact that their populations are already in decline - could have devastating consequences.

According to a recent article in the scientific journal, Plant Pathology, in July 2022: ‘Cypress canker has been known in South Africa for many decades, where it causes a serious disease on non-native species of Cupressus, but it has never been found on native Cupressaceae. The newly discovered disease caused by a probable alien pathogen is of particular concern because only three species of Widdringtonia occur in South Africa and they are important components of the native flora.’ (

Source Fabi News – All photos courtesy of Fabi.

A sick and dying Italian cypress in Welkom with a severe case of cypress canker fungus disease.
Janneke Aylward and Mike Wingfield of Fabi recently discovered the presence of the canker on Italian Cypress trees growing on the University of Pretoria campus.
Iconic Welkom cypress trees.

In search of a biocontrol for the Shot Hole Borer

Dr Wilma Nel and Garyn Townsend with collaborators in Vietnam collecting PSHB infested material.

Since it was discovered in KwaZulu-Natal in 2017, the Polyphagous Shot Hole Borer (PSHB) (Euwallacea fornicates) has spread rapidly into every province in South Africa except Limpopo, and has infested thousands of trees in urban areas, native forests and more recently in fruit crops.

This tiny invasive ambrosia beetle, native to Southeast Asia, has set alarm bells ringing as it is able to infest a wide variety of tree species – including seemingly strong, healthy trees - and is capable of spreading far and wide with the aid of human activity. It bores into the sapwood of trees and brings a damaging fungus, Fusarium euwallaceae, along with it.

The economic impact of PSHB in South Africa is still in its infancy, but is expected to run into the billions if allowed to continue unchecked. The environmental impacts are also potentially huge as a number of native trees are susceptible to infestation.

The Polyphagous Shot Hole Borer … pest invader spreading rapidly across South Africa.

One of the management options being explored by scientists at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, is to identify a natural enemy of PSHB in its native range and then introduce it into South Africa where it could play a role in controlling the PSHB population.

This led to a recent trip to northern Vietnam by Prof Brett Hurley and Dr Wilma Nel of FABI and PhD candidate Garyn Townsend to collect material from trees infested by PSHB with the aim of finding, identifying, rearing and testing natural enemies. The visit was highly successful and the team brought PSHB-infested Acacia back to the FABI quarantine facility, after obtaining the required permits from South Africa and Vietnam.

The plan is to monitor the material for the emergence of natural enemies, specifically parasitoids, which could be reared and deployed in South Africa to serve as an effective biocontrol agent for PSHB. This is a lengthy process that involves extensive testing to ensure that the introduced species is sustainable and does not cause any collateral damage to native species in South Africa.

Prof Brett Hurley, Dr Wilma Nel and Garyn Townsend with collaborators at the Vietnamese Academy of Forestry Sciences in Hanoi, Vietnam.

The project has been made possible through the funding of the Department of Forestry, Fisheries & the Environment and through collaboration with the Vietnamese Academy of Forestry Sciences, specifically Prof Pham Quang Thu.

According to a recent article in the South African Journal of Science by a group of FABI scientists, the South African PSHB invasion represents the largest outbreak of this beetle in its invaded range anywhere in the world. It has infested 130 plant species in urban, agricultural, and native ecosystems in South Africa, including 44 previously unreported hosts.

In South Africa, PSHB is currently mostly confined to urban environments, but its presence has also been confirmed in the natural forests around Knysna and George where it is feared it could do extensive environmental damage.

Virgilia oroboides, a native tree species found in the southern Cape natural forests, is a reproductive host for PSHB.

PSHB infected tree showing damage from the fungus.

“It is an important pioneer forest species in the southern Cape that protects forests from severe climatic fluctuations and fire and houses a large number of native organisms. Elimination of this single species could have irreversible consequences for native forest integrity,” the scientists write. 

PSHB control measures using pesticide sprays have been effective in laboratory conditions, but are currently not considered practical in the wild. Deployment of a biocontrol agent looks to be the best management option at this stage, provided a suitable candidate can be found, and the necessary authorisation for its release in South Africa obtained.

The only agricultural crops that appear to be affected by PSHB so far are pecan and macadamia, but they are not reproductive hosts and so the impacts are expected to be limited. Other orchard crops that may be vulnerable to PSHB are cherry, apple, citrus, peach, guava, olive, grape and prune crops.

Initial surveys in invaded urban areas of Johannesburg, Knysna, George and Somerset West indicate that a high percentage of English oak, London plain trees, box elder and other maples will die when infested by PSHB. The cost of disposing of these urban trees and replacing them will be considerable.

Urban trees play a vital role in providing shade, moderating temperatures and creating an attractive environment that enhances the quality of life and boosts the hospitality and tourism sectors. They also provide refuge for numerous birds and insects.

The team in the quarantine facility at FABI, University of Pretoria, where the collected material is being monitored for emergence of natural enemies of PSHB.

How to detect PSHB infestation

The first signs of PSHB infestation are the presence of tiny holes penetrating the bark of trees and leading directly into the sapwood. These random holes, less than 1mm in diameter, look a bit like they could have been caused by shotgun pellets – hence the common name ‘shot hole borer’.

Lesions, wet patches and gum exudation may be visible on the outside of the tree, and a pinkish-brown stain caused by the associated fungusmay be seen spreading from the gallery into the vascular tissues below the bark. PSHB colonisation of reproductive hosts often results in wilting and death of the infested branch - or the entire tree.

The FABI team has had a lot of success with the introduction of biocontrol agents for a number of tree pests in South Africa in the past, and this experience will be invaluable in finding an effective biological enemy for PSHB. The stakes are high as this tiny hitchhiking beetle continues to spread across southern Africa.

Typical Eucalyptus plantation in Vietnam.


FABI News;

Article by W. Nel, B. Slippers, M. Wingfield, N. Yilmaz & B. Hurley in South African Journal of Science, April 2023

All photos courtesy of FABI.

Potential new biocontrol for Gonipterus

Gonipterus snout beetles are leaf feeders. The adults feed on the edges of mature leaves causing defoliation of the tree crowns and stunted growth. Studies have shown that 50% crown defoliation can result in up to 85% loss of wood production over a 10 year period.

The Forestry and Agricultural Biotechnology Institute (FABI) team is testing a tiny fly that could turn out to be an important new biological control agent of the Gonipterus snout beetle, currently the most serious insect pest of Eucalyptus trees in South Africa.

The potential new biocontrol agent is a tachinid fly, Anagonia cf. lasiophthalma, which parasitizes the larval stage of the Gonipterus beetle. The flies were sourced from the Forest and Paper Research Institute in Portugal, which has been studying this insect for its potential use as a biocontrol for Gonipterus species for some time.

The parasitoids were imported into the FABI quarantine facility at the University of Pretoria and are showing great promise as an effective biocontrol for Gonipterus sp. n. 2, which is causing significant damage to Eucalyptus plantations across all major forestry regions in South Africa.

Anagonia cf. lasiophthalma is a potential new biocontrol agent for the Gonipterus snout beetle, currently damaging Eucalyptus trees in South Africa and neighbouring countries.

Gonipterus beetles are native to Australia. They were first identified in South Africa in 1916, rapidly spreading across the country and into neighbouring territories. This led to the release in 1926 of Anaphes nitens – a tiny wasp - which was the first biocontrol agent in South African forestry. Anaphes nitens was effective in controlling the spread of the Gonipterus beetles, but in the past few years damage from Gonipterus infestations has been increasing once again and it has become clear that on its own Anaphes nitens is not sufficient to suppress Gonipterus populations.

This has led to renewed interest in Gonipterus in South Africa and the discovery that it is not a single species, but one of several different taxa. Hence the one currently doing the damage in South Africa has not even been formally named yet.

Initially it was not known whether the fly Anagonia cf. lasiophthalma would parasitize Gonipterus sp. n. 2, the species present in South Africa, and whether it would be possible to rear it in quarantine. However, work at the FABI facility led by technical assistant Amy Collop and supported by Samantha Bush, Michelle Schroder and Brett Hurley, has confirmed that Gonipterus sp. n. 2 is a host of this parasitoid and the initial stages of a lab-reared population of the flies has been established.

This is very exciting news, according to the FABI team, as it confirms the possibility of using this parasitic fly as a biological control agent for Gonipterus - although there is still much work to be done before it can be safely released into the field.

According to Brett Hurley of FABI, what makes Anagonia especially exciting is that it parasitizes a different life stage of Gonipterus, namely the larvae, as compared to Anaphes which is an egg parasitoid. Thus it is more likely to add to the overall control of Gonipterus, as compared to releasing another agent that targets the same life stage.

Gonipterus larval stage. The larvae feed on the epidermis and mesophyll of young Eucalyptus leaves.

“The first step before releasing Anagonia in South Africa was to confirm that it would parasitize Gonipterus sp. n. 2 - this has now been done,” says Brett. “The second step is to establish a rearing population for experiments - this is ongoing. The third and very important step is to conduct host specificity tests, i.e. to assess if Anagonia will attack other native insects. This is the step where it is difficult to say how long it will take - it could be one year or it could be 3+ years, it depends on multiple factors such as our success with rearing the different insects needed for these studies. If the tests indicate that Anagonia is specific to Gonipterus and therefore safe to release, then we move to step 4 - applying to the government for permission to release Anagonia into the field. This application would be sent for comment from national / international researchers before a decision is made,” he said.

A number of Eucalyptus species, varieties and clones are negatively affected by Gonipterus including E. dunnii, E. grandis, E. nitens, E. urophylla, E.smithii and GUs.

Gonipterus is not the only pest on the FABI team’s radar, as there are many new potential insect pests and pathogens on the horizon!

“We are currently investigating the most likely future insect pests of eucalypts. One insect pest that is moving around, e.g. recently reported in Portugal and South America, is the eucalypt leaf feeding beetle, Trachymela sloanei. But the reality is that many of the new pests and pathogens are not currently known in their native range or anywhere in the world, so it is very difficult to predict,” concluded Brett.

Amy Collop busy rearing Anagonia cf. lasiophthalma in a petri dish at the FABI facility in Pretoria.