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While crop rotation has been around for centuries, soil health is a new topic in recent agricultural discussions. Despite the long history of agriculture and different farm management techniques, the focus of agricultural research has largely been on maximising profit and yield at any cost. With global issues such as overpopulation, water scarcity, climate change and land availability high on the agenda, developing more sustainable agricultural practices is currently occupying the forefront of research.
Sustainable soil management is one such practice that is gaining more focus. Various soil management practices are available and effective, depending on the end goal that needs to be reached. Determining which soil management practices would best suit your land can be assisted by evaluating the state of your land’s soil health.
Soil health can be defined as the ability of soil to function within an ecosystem as an essential living system to maintain or improve plant and animal productivity, as well as water and air quality, and promote plant and animal health. There are many tests available that can be used to assess soil health. Depending on what properties or factors need to be focussed on, soil health and quality tests can include chemical, physical or biological tests or tests that combine the different properties. Concerning soil biological tests, the three main focus areas are soil diversity, soil activity and soil functionality.
Soil diversity and activity
Soil diversity tests identify what macro- and micro-organisms are in the soil, while soil activity and functionality tests focus on what these macro- and micro-organisms use and produce, and what activities are carried out due to the population diversity. To date, microbial analysis in the Eastern Free State trial has been focussed on microbial activity and functionality, mainly due to the higher costs involved in microbial diversity testing.
Soil health can be directly impacted by agricultural practices such as crop rotation, which can in turn directly impact the profitability of dryland crop production and the financial risk involved. Therefore, the long-term aim of this study is to evaluate and optimise crop rotation systems for potato production in the Eastern Free State to improve soil health, soil physical and chemical conditions, and profitability of dryland potato production in the region.
The soil chemical and physical responses to different soil rotation programmes were presented in a previous article (CHIPS Nov/Dec 2024). In this article, we report on the soil microbial responses to different crop rotation programmes in the Eastern Free State dryland study.
Procedures
A long-term trial commenced during the 2014/15 summer season in the Petrus Steyn district of the Eastern Free State, consisting of four five-year crop rotation systems, as shown in Table 1. By the end of the first complete cycle of five years, few differences had occurred between crop rotation systems, mostly seen in a slight shift in soil chemical properties.
Table 1: Crops in the four five-year crop rotation systems. Note the replacement of maize by a cover crop in year seven (Rotation 1), the replacement of teff by maize in year eight (Rotation 1), as well as the inclusion of a cover crop mixture in year nine (all rotations).
| Calendar year | Rotation year | 1 | 2 | 3 | 4 |
|---|---|---|---|---|---|
| 2015/16 | Year zero | Potatoes | Potatoes | Potatoes | Potatoes |
| 2016/17 | Year one | Maize | Maize | Maize | Maize |
| 2017/18 | Year two | Maize | Sugar bean | Soya beans | Sunflower |
| 2018/19 | Year three | Teff | Maize | Maize | Maize |
| 2019/20 | Year four | Fallow | Fallow | Fallow | Fallow |
| 2020/21 | Year five | Potatoes | Potatoes | Potatoes | Potatoes |
| 2021/22 | Year six | Maize | Maize | Maize | Maize |
| 2022/23 | Year seven | Cover crop | Sugar bean | Soya beans | Sunflower |
| 2023/24 | Year eight | Maize | Maize | Maize | Maize |
| 2024/25 | Year nine | Fallow/cover crop | Fallow/cover crop | Fallow/cover crop | Fallow/cover crop |
| 2025/26 | Year ten | Potatoes | Potatoes | Potatoes | Potatoes |
It was consequently decided to replace maize with a mixture of cover crops in Rotation 1 from year seven to determine whether the organic matter content of the soil could be increased as a result. Furthermore, in year nine (2024/25 season), one half of the plots will remain fallow according to the original plan, while the other half will be planted to a mixture of summer cover crops.
Cover crops have the potential to control erosion, reduce nutrient leaching, increase water infiltration, suppress pests and diseases, and improve soil quality due to increased microbial activity in the soil, which in turn can ensure that agricultural practices are more sustainable.
Soil samples from the rhizospheral topsoil (0 to 25 cm depth next to plants and their roots) were taken at the three-time points per season for biological soil analysis – at the beginning of the season after crop emergence (October to November), the middle of the season (February to March), and the end of the season before harvesting (May to June).
Since the 2022/23 season, soil biological properties have been analysed for soil microbial functionality using Biolog EcoPlates®, which measures microbial activity as a result of different carbon source usage. Microbial functionality is expressed as EcoPlate Average Well Colour Development (AWCD), where a greater colour change indicates higher microbial activity concerning a specific carbon source usage.
Soil microbial activity in the form of carbon dioxide release (microbial respiration) was also measured, using the Cornell Soil Health Laboratory potassium hydroxide (KOH) method, and the Solvita® CO2 Burst test method.
These two methods were used to assess microbial respiration levels. The Solvita test allows for rapid microbial respiration results but can be more costly. The KOH method measures respiration after four days when respiration levels should become more consistent, but it requires the correct chemicals, equipment and calculations. While the two tests are not directly comparable due to differing incubation periods and subsequent results (ppm CO2), the trend of the results remains relatively unchanged between the two test methods.
Results
The most important biological property results of the 2023/24 growing season are presented, as well as the microbial activity (Biolog EcoPlate results) for the 2022/23 growing season when cover crops were first incorporated into the trial.
The microbial functionality (AWCD) of the cover crop rotation (R1) was the highest of the four treatments at the start and end of the 2022/23 growing season (Figure 1). Similarly, by the end of the 2022/23 growing season, the activity in the sunflower rotation (R4) had increased substantially compared to that of the soya bean (R3) and sugar bean (R2) rotations. Following a dormant winter period, the microbial activity levels for the start of the 2023/24 growing season had increased in R2 and R3, compared to the decrease in R1 and R4. By the end of the growing season, the activity in all rotations had increased from the beginning of the season, with R4 (following sunflowers) maintaining the highest activity levels of all four rotations.
Figure 1: The AWCD for each of the four crop rotation systems, over the three seasonal time points (beginning, middle, and end of the season) for the 2022/23 season (cover crop inclusion) and the 2023/24 season (maize).
Notably, the microbial functionality in all four rotations was higher at the beginning and end of the 2023/24 season when compared to the activity at the beginning and end of the 2022/23 season. Overall, the higher activity in Rotation 1 throughout the two growing seasons may be attributed to the inclusion of cover crops in the 2022/23 season. Microbial functionality levels averaged across the different growing seasons and sampling time points indicated that overall activity in R1 (following cover crops) was the highest (0.554 units), followed by R4 (sunflower – 0.536 units), R2 (sugar beans – 0.494 units) and lastly R3 (soya beans – 0.471 units).
Throughout the 2023/24 growing season, the microbial respiration levels in the rotation following cover crops (R1) were consistently higher compared to the other rotations (Figure 2). All four rotations experienced a substantial increase in respiration from the beginning to the middle of the growing season, decreasing again by the end. The greatest level of respiration recorded was mid-season in R1 following cover crops (53 221 ppm CO2), while the remaining three rotations measured above 40 000 ppm CO2. The lowest respiration level recorded was at the end of the season in R3 following soya beans (11 002.50 ppm CO2).
Figure 2: Average soil respiration (ppm CO2) recorded for each of the rotations (cover crop/maize, sugar bean/maize, soya bean/maize, sunflower/maize), for the beginning, middle, and end of the 2023/24 season.
Respiration levels in R1 following the cover crops were on average 9 647 ppm CO2 greater than that of the other three rotations throughout the 2023/24 growing season.
In general, the microbial activity levels were consistently higher in the middle of the season when compared to the beginning and end of the season. The substantially lower activity levels recorded for the beginning and end of the season compared to that of the middle of the season could be attributed to the seasonal period.
The beginning of the season is expected to have lower microbial activity following the dormant winter or non-growing season compared to the middle of the season, as microbes have been more active throughout the plant’s growing season, likely as a result of increased water and nutrient availability due to the presence of the growing crops.
When considering the microbial results, the inclusion of the cover crops resulted in a desirable increase in soil microbial activity. These results pose a new question: Which microbes are becoming more active? Further analysis into the soil diversity, with regard to the identification of the microbial populations in each rotation, may assist in explaining the differences in respiration levels and microbial activity between the different rotations and sampling time points, as well as to determine if the activity can be attributed to the increase in natural microbial populations in the soil due to the cover crop inclusion, or if it is related to pathogens that may remain active in the soil.
Summary and conclusions
These findings indicate that the incorporation of cover crops can greatly impact the biological soil properties and overall soil health and quality. The incorporation of cover crops into rotation systems and the soil can increase soil microbial diversity and subsequent activity and functionality, thereby allowing microbial communities to self-regulate through a greater diversity of species and create more disease-suppressive soils using a higher microbial diversity and subsequent competition for nutrients.
By creating microbial competition for nutrients, the beneficial or neutral microbes can outcompete pathogens, thereby reducing pathogenic incidence and disease levels in the soils. Cover crops also provide other benefits such as natural fertilizers and pesticides, while also creating the opportunity for producers to increase their income by using the above-ground material of the cover crops as livestock feed. – Taryn Armfield, Prof Martin Steyn, Dr Elsie Cruywagen, and Prof Quenton Kritzinger
For more information and sources, send an email to martin.steyn@up.ac.za, armfieldtaryn@gmail.com, cruywagenem@arc.agric.za, or quenton.kritzinger@up.ac.za.