Soil microbiology testing involves analysing the microbial communities within the soils, including bacteria, fungi, nematodes, and other organisms. Healthy soils are teeming with beneficial microbes that support nutrient cycling, suppress disease, and improve soil structure. Conversely, imbalances in microbial communities can lead to yield loss and an increased susceptibility to disease.

Pathogen testing focuses on identifying disease-causing organisms that may threaten vegetable and onion crops. Most pathogens that cause soilborne diseases, for example, survive in the soil, waiting to infect the root system of vegetable and onion crops.

For some pathogens, the quantity of inoculum in the soil is strongly related to the risk of disease occurring, therefore pathogen testing can aid in the establishment of disease risk thresholds.

Several organisations provide soil microbiology and pathogen testing services in Australia. Here’s a closer look at some of the prominent providers: Metagen Australia, South Australian Research and Development Institute (SARDI), Eurofins APAL and Microbiology Laboratories Australia.

Metagen

Metagen is an Australian private agricultural biotechnology company offering advanced soil testing services, including microbial DNA soil testing, soil enzyme testing, and soil chemistry testing.

Soil microbial DNA testing

Metagen uses robotised polymerase chain reaction (PCR) facilities to extract DNA and analyse microbial communities in the soil. The DNA microbial soil test ‘fingerprints’ the microbes in the soil, allowing for confirmation that management practices used on-farm are leading to positive changes in microbial communities.

If, however, low levels of beneficial microbes are detected, it can highlight the need to change soil management practices. Growers can utilise the results of this microbial soil test to measure improvements in soil microbial health over time. The DNA test also has the capacity to detect potential pathogens associated with poorly performing paddocks.

Soil enzyme test

Microbes can convert soil compounds containing nutrients such as calcium, nitrogen, and phosphorus, among others, into forms available for uptake by them and plants. To do this, microbes produce enzymes that break up the compounds.

Metagen’s soil enzyme test measures the activity of enzymes produced by microbes in the soil, providing an indication of how well soil microbes are functioning. This is important because the soil DNA test detects soil microbes independently of how well they are doing. The soil enzyme test, included as part of Metagen’s comprehensive soil health test, helps growers fine-tune management practices to support healthy microbial activity.

Soil chemistry testing

Metagen offers soil chemistry testing to identify nutrient deficiencies and imbalances. This analysis helps growers optimise their crop nutrition programs.

Pathogen isolation and identification

Visual diagnosis of plant diseases can often lead to misdiagnosis and the implementation of suboptimal management practices. Metagen offers a plant pathogen and identification service to help growers better understand the disease pressures in their crops. The test isolates plant pathogens from infected plant material using traditional microbiological techniques and identify pathogens using microscopy and DNA sequencing.

Nematode Diagnostic service

Monitoring for levels of plant parasitic nematodes prior to planting a susceptible crop can help inform decisions on whether expensive nematicide treatments are required. Metagen processes soil samples to recover nematodes which are then identified by microscopic analysis. Results of this test are delivered in a final report.

South Australian Research and Development Institute (SARDI)

SARDI, the research arm of the Department of Primary Industries and Regions, South Australia, provides molecular diagnostic (DNA) testing services for soilborne diseases for several industries, including horticulture, through the Molecular Diagnostic Centre (MDC).

SARDI uses the PREDICTA testing technology to quantify the level of DNA of specific disease-causing pathogens in a sample of soil. Due to its specificity and sensitivity, the technology can detect low levels of multiple pathogens from the same sample. DNA levels are reported to growers, allowing them to identify which soilborne pathogens pose a significant risk to their crops prior to planting and make informed management decisions. The current suite of tests available for vegetable growers is well-matched for use in brassica, carrot, capsicum, onion, and potato production.

PREDICTA can be used to quantify pathogen levels at any stage of the cropping cycle, enabling growers to conduct not only pre-plant assessments, but also in-crop assessments for monitoring pathogen level changes, evaluating how management practices effect infection and pathogen inoculum levels, and establishing disease risk thresholds. Extracted DNA can be further used for other downstream applications, such as microbial profiling and analysis of beneficial microorganisms.

SARDI also offers training and accreditation for agronomists to understand and interpret results, and correctly collect soil samples. Correct sampling is essential to obtain meaningful results, as pathogens are not evenly distributed across paddocks.

Eurofins APAL

Eurofins APAL offers independent soil, plant and water analysis services. Whilst Eurofins APAL doesn’t directly offer soil microbiology and pathogen testing, they have a working relationship with a number of laboratories across Australia that they collaborate with, including SARDI and Microbiology Laboratories Australia.

Soil biological testing

The soil biological test involves identifying microbial activity in the soil through the measurement of CO2 emitted by soil microbes over time. Higher CO2 emissions correlate with more active microbial communities, and in turn healthier and more fertile soil, a prerequisite for good plant health.

Soil fertility analyses

Eurofins APAL also provides comprehensive soil fertility analyses, helping growers address physical and chemical soil imbalances. Their testing services can guide decisions on fertiliser applications and soil amendments.

Microbiology Laboratories Australia

Microbiology Laboratories Australia (MLABS) is a company offering microbiology and soil health analysis for private, commercial and government organisations across Australia.

Microbial Biomass by cell wall profiling (PLFA)

MLABS conducts microbial biomass by phospholipid fatty acid (PLFA) analysis. The PLFA analysis measures the living biomass of key microbial groups important for soil health and productivity, such as nutrient cycling (nitrogen, phosphorus, etc), disease suppression and residue breakdown.

Next-generation sequencing

Next-generation sequencing technology allows for the analysis of most of the microbial species in a single test, which can then be used to detect diversity, functions and good and bad interactions in the soil. The test can identify nearly all bacteria and fungi present in a sample, including any potential or unknown pathogens.

Count Wise

The Count Wise test quantifies key culturable microbes that promote plant growth and offer biocontrol benefits. It reports on total bacteria, fungi, Actinomycetes, Bacillus, Trichoderma, and the ratio of bacteria to fungi colony-forming unit ratio and diversity. The results provide growers with a snapshot of their soil’s microbial diversity and health.

Nem Wise

The Nem Wise test measures plant-parasitic nematodes, which can damage roots and create entry points for diseases. It also identifies beneficial free-living nematodes that support nutrient cycling and suppress plant pathogens.

VAM Wise

Vesicular Arbuscular Mycorrhiza Fungi (VAM) are critical to soil health. They improve nutrient cycling, plant water uptake, disease resistance, and soil structure. The VAM Wise test measures the presence of VAM spores in the soil and/or inside the plant roots to assesses their contribution to plant and soil health.

Under ideal conditions VAM spreads rapidly throughout the root system of host plants, providing an efficient extension of its root systems and increasing nutrient uptake. This test is particularly useful for detecting conditions like long fallow disorder.

Soil Carbon, Phosphorus and Nitrogen Wise

The Soil Carbon, Phosphorus, and Nitrogen Wise tests provide growers with valuable insights into how the cycle of these nutrients is influencing the uptake, solubilisation and sequestration of fertilisers, composts, etc. by the plant and soil. This test combines microbiology and nutrient analysis to evaluate the carbon, phosphorus, and nitrogen pools in your soil, and shows the rate at which nutrients are likely to be available to plants under current field conditions, giving growers a clearer picture of nutrient availability and soil health.

CropSaver and Plant Pathogen Testing

Plant tissue and soils can both be tested for plant pathogens by Next Generation Sequencing as mentioned above, by ELISA (enzyme-linked immunosorbent assay), which uses antibodies specifically built to detect Pythium, Rhizoctonia and Phytophthora, or by PCR (incubating lab-growth plants) to make sure that only active, infective pathogens are detected and reported.

Conclusion

Soil microbiology and pathogen testing allows growers to gain insights into their soil’s microbiological and chemical composition. As soil testing technologies continue to evolve, growers have more opportunities to optimise their soil management strategies to maximise crop productivity.

Soil microbiology testing is especially valuable for identifying risks such as pathogen levels or low incidence or activity of beneficial microbes.

Differently from a soil chemistry test, a soil microbiology test does not allow for specific management recommendations. However, poor soil microbiology commonly signals a lack of microbe ‘food’, i.e. organic matter.

Similar to soil chemistry tests, soil microbiology and pathogen testing should be used to monitor soil health trends and the impact of management changes rather than as a ‘on-off’ test for trouble shooting.

FURTHER READING
soilwealth.com.au/2020/10/what-you-need-to-know-about-soil-microbiology