Comparing soil microbial diversity in organically and non-organically farmed soils
Why this project:
Microbial life in agricultural soils is known to react to management sytems; including to the use of pesticides and fertilisers. Conversely, microbial life influences the uptake of nutrients from the soil. Hence, identifying whether there indeed is a difference in microbial life between soils managed under an organic system and one that is commonly used in agriculture in that area may well provide indications of why an organic system works in that area and which practices within the organic system are likely to be most beneficial (for more details see background).
Microbial populations in organically farmed soils have often been reported to be greater and more diverse than in soil farmed conventionally. This was recently confirmed by the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment in Switzerland1.
In Australia, the ‘Biomes of Australian Soil Environments’ (BASE) project (http://www.bioplatforms.com/soil-biodiversity/) has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. The database, covering over 900 sites, includes also agricultural soils (pasture, cotton, wheat, sugar, apples) but without differentiating between agricultural production systems.
The work currently under way in Australia and overseas provides a unique opportunity to build on established knowledge and to use the existing framework and infrastructure to obtain and assess the microbiome of organically farmed soils in Australia and compare them with nearby soils from conventional farms and unfarmed (natural) land. This comparison, which will include soils from WA, VIC and QLD will show whether the differences found in Switzerland are also evident in Australian conditions, and if so, if observed differences are apparent in all analysed organic soils or only in certain circumstances.
It is envisaged that four organic farms, representing wheat, pasture, vegetable and tree crop production, will be selected each in WA, VIC and QLD, so that samples can be taken also from conventional neighbours and unfarmed land. Hence, each location will comprise three distinct sampling areas (organic/conventional/natural), each of which will host three sampling quadrats (25 m x 25m). Sampling and analysis (DNA extraction and sequencing, soil physico-chemical analyses) will be done according to the methodologies established for BASE 2. If samples and ensuing results are uploaded into the BASE database, soil and DNA samples will be also archived for future use.
Although organic farming systems have always relied on healthy soil ecosystems with diverse microbial populations to maintain productivity, the increased R&D focus on soil microbial communities, root – microbe interactions, and the use of specific microbial agents will benefit not only conventional but also organic farmers. Projects like this will for example (i) identify microorganisms that are particularly efficient in enhancing phosphorus solubility in different soils amended with various organic inputs, (ii) monitor the transformation of microbial populations within crop sequences, or following cultivation or the use of organic soil amendments, or (iii) help manage the soil environment by means of promoting beneficial and suppressing detrimental organisms.
Results of the proposed project will be published in a scientific journal and also in a report for OTARE.
Prof Andy Whiteley, University of Western Australia
Dr Paul Dennis (tbc), University of Queensland
Johannes Biala, University of Queensland
Dr Pauline Mele (tbc), Dept of Agriculture, Victoria.
Professor Andy Whiteley from the University of Western Australia (UWA) is in the process of creating a map showing the diversity and distribution of microbial life in soils across Western Australia. He uses citizen scientist to supply soil samples from across the state and DNA sequencing to identify the biodiversity of microbes in these soils. This information is then used to build a state-wide map detailing the biodiversity and health of WA’s environment. The outcome of this ‘MicroBlitz’ (https://www.microblitz.com.au/) will be a baseline map and a point of reference that can be shared and used to monitor, manage and protect WA’s environment into the future. The map is intended to inform strategies and initiatives to address big-picture sustainability issues, such as climate change and food security.
Microbial populations in organically farmed soils have often been reported to be greater and more diverse than in soil farmed conventionally. This was recently confirmed by the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment in Switzerland (Hartman et al. 2014)1. The work currently under way in WA provides a unique opportunity to build on existing knowledge and to use the existing framework and infrastructure to obtain and assess the microbiome of soil samples from a range of organic farms that differ in geographic location, environmental / climatic conditions, soil type, agricultural enterprise, management, etc. Comparison of these soils with conventionally farmed soils from across WA will show whether the differences found in the DOK trial in Switzerland are also evident in Australian conditions, and if so, if these differences are apparent in all analysed organic soils or only in certain circumstances. Likewise, the dataset of organic soils can be also compared to soils from non-farmed environments to see similarities or differences.
Hartman M, Frey B, Mayer J, Mäder P, Widmer F (2015). Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal, 9, 1177–1194.
Bisset A, et al. (2015). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5, 21.