Study shows pathogens lurking in farm and forest soil

30 July, 2019

Cutting-edge science has revealed for the first time what microbes are lurking in our soil – and that there are many more harmful ones on farms and in plantation forests than in natural forests.

In his PhD research with the Bio-Protection Research Centre, based at Lincoln University, and Manaaki Whenua – Landcare Research, Andi Makiola studied how land uses such as farming and plantation forestry affected the variety of plant pathogens in the soil and on plant leaves and roots.

Pathogens are organisms that can cause plant disease; they include fungi, bacteria, and oomycetes (for example, Phytophthora agathidicida, which causes kauri dieback).

Dr Makiola and colleagues used a new method called next-generation sequencing to extract and amplify DNA from soils and plants across New Zealand, revealing what plant pathogens lived in them.

His results, published online in the journal Molecular Ecology, show there are many more species of plant pathogens in land that’s been modified by pasture, cropping, and plantation forestry than there are in natural forest.

That applies only to pathogens, not to all microbes, including the beneficial ones. “We find no evidence of land use type being a consistent driver for the alpha-diversity of all fungi, oomycete and bacteria,” the authors wrote.

Several factors may contribute to the increased variety of pathogens in farm and forestry soil. These include:

• Monocultures, which can help pathogens spread more easily

• Rapidly growing cultivated crops, which are more susceptible to pathogens than slower-growing naturally occurring plants

• Excessive fertiliser use (especially nitrogen) and irrigation, which can benefit pathogens

• Soil disturbance and pesticide use, which can suppress beneficial micro-organisms and promote plant pathogens.

Molecular tools such as metabarcoding (using next-generation sequencing) are revolutionising scientists’ understanding of microbes, said co-author, and one of Dr Makiola’s PhD supervisors, Prof Ian Dickie, of the University of Canterbury.

“For the first time we can study pathogens in seemingly healthy ecosystems,” he said. “We don’t have to wait until we see disease symptoms to find out what’s there.

“Andi’s study was the most widespread sampling of potential pathogens ever carried out in New Zealand, and gives scientists entirely new insights into where pathogens exist, and how pathogen communities are structured.

“It’s quite surprising that exotic plants host such a high diveristy of potential pathogens,” Professor Dickie said. “This may represent a risk of pathogen populations building up on exotic plants and spilling-over into native ecosystems.”

The authors say the results open the way for studying how natural ecosystems inhibit plant pathogens.

“Our results suggest that the metabarcoding approach could be a useful tool to study the drivers of pathogens at large scale, necessary for appropriate prevention and management strategies and for a sustainable provision of future ecosystem services and agroecosystem productivity.”

Dr Andi Makiola now works at INRA (Institut National de la Recherche Agronomique), France.

Land use is a determinant of plant pathogen alpha but not betadiversity, https://doi.org/10.1111/mec.15177

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