Determining the risk of mulches in the spread of canker pathogens in apple orchards

The use of mulches is an important practice in the industry. The aim of this study was to gain a better understanding of the risk of canker pathogens being spread from mulch material made from orchards to be removed, but also from pine chips and straw. The objectives include: to identify the pathogens associated with apple orchards destined to be removed; develop molecular detection protocols for major canker and wood rot pathogens; determine occurrence of pathogen spores in runoff water from mulches (fruit tree wood chips, pine chips or straw) and lastly to monitor spore dispersal patterns from the different mulch types.

Dieback branches of apple trees of orchards destined to be removed were sampled from 14 orchards in the Grabouw, Vyeboom and Koue Bokkeveld apple-producing regions. Isolations were made and fungal species identified. Mulch made from removed apple trees were collected from heaps and also from the berms of apple orchards. Fungal structures were identified and water washings made from which the major canker and wood rot species were detected with quantitative PCR. The identity and viability of the fungal structures were determined by making cultures from the spores. At first only apple mulch were collected and analysed for Diplodia seriata (2021). Thereafter sampling included apple chips, pine chips and straw and sampling was done over two years (2022 and 2023). Washings were made of all three mulch type samples and qPCR detection for four pathogens (Cytospora  schulzeri,  Diplodia seriata, Eutypa lata and Schizophyllum commune). Diplodia seriata spore dispersal was monitored for six orchards over two years including orchards with apple wood chips, pine chips and straw as mulch. Spore trapping was done weekly with Vaseline coated glass slides and rotorod samplers in 2022 and 2023.  Washings were made from the slides and rods, DNA extracted and qPCR analyses conducted to detect Diplodia seriata. A pilot and second larger sentinel tree trial was conducted by placing wounded young Cripps Pink apple trees in three orchards with apple mulch, as well as control trees, to assess wound infection

Fungi associated with canker and wood rot symptoms were isolated from 118 of the 144 trees showing symptoms of dieback. Of the Ascomycota fungi, Eutypa lata was most often isolated (from 18.6% of trees) followed by Diplodia seriata (9.3%). The predominant wood rot pathogen associated with the dieback of apple trees was Trametes versicolor (from 33.1% of trees). Viable Diplodia seriata cultures were obtained from 87% of the mulch wood pieces investigated. Diplodia seriata remained present and viable for a period of 20 months on the wood chips. To be able to detect Diplodia seriata qPCR primers were developed which had a limit of quantification of 2859 fg/µl and limit of detection of 571 fg/µl. From the 2021 apple wood mulch collections DNA was extracted from water-washes of 120 wood piece samples and D. seriata was detected from 101 of these samples. From apple and pine chips samples the most common species was D. seriata. In 2022, 43.3% of both apple chips and pine chips samples had fruiting structures of D. seriata. In 2023, 42.5% of apple chips and 35% of pine chip samples had fruiting structures of Diplodia seriata. Cytospora schulzeri was found on 20% of pine chips samples collected from orchards from Ceres in 2022. Other pathogens were found more infrequently. Pathogen detection in wash water showed that for 2023 Diplodia seriata were found from apple chips (40%) and pine chips (30%), significantly more than from straw (2.5%). Other pathogens detected in wash water were found at low incidences: Cytospora  schulzeri (4.6%), Eutypa lata (4%) and Schizophyllum commune (1.4%). Results from wash-water of pruning debris showed that Diplodia seriata and Cytospora schulzeri occurred more often and  Eutypa lata and Schizophyllum commune occurred infrequently. Spore trapping was done for 21 weeks in 2022 and 18 weeks in 2023. Apple chip mulch had significantly more spore release events, namely 65%, in comparison with pine chips (28%) and straw (15%). Straw do not harbour fruiting structures of the pathogens, but due to the presence of pruning debris, spores were trapped in these orchards. Diplodia seriata was isolated from the pilot sentinel tree trial and 13.33% of all isolates of the second trial were D. seriata. Wound infection of sentinel trees varied from 3.33% to 16.67%, indicating that wounds can become infected with canker pathogens.

This study showed that apple trees to be excavated and used for mulch mainly harbor fruiting structures of Diplodia seriata. Spores of Diplodia seriata are mainly released from June to September, during the period of winter pruning. Wounds can get infected with D. seriata, but can remain latent and could cause cankers if environmental stress factors are conducive.  Spore trapping clearly showed that pine chips harbour less viable Diplodia seriata structures. From an orchard phytosanitary perspective, straw would have the least risk, followed by pine and apple chips. If pruning debris has fungal fruiting structures it should rather be removed from the orchard floor, since it can be a source of Diplodia seriata spores.

Mulch made from diseased apple orchards has a risk for the spread of Diplodia seriata. Pine chips also had fruiting structures of Diplodia seriata, but much less spore release events were recorded. In general, old orchards with high levels of dieback should be avoided for chipping and use as mulch.