Cultivation technique and soil microbiota

Is the microbiota of cultivated soil influenced and modified by the farming techniques applied? The answer is certainly affirmative. But the ways in which this happens are not yet fully known.

In a general sense, it is believed that among the techniques that can positively influence the soil microbiota are crop rotation, the use of organic fertilizers and cover crops and the reduction of tillage.

On the other hand, chemical fertilization (if it leads to imbalances in the soil composition), the use of pesticides and intensive processing, are considered practices that are potentially harmful to the microbial balance of the soil.

But is everything really so simple and linear? Not really, especially when trying to understand and measure the combined effect of multiple variables. Here’s what research conducted on the subject tells us.

The use of fertilizers and pesticides is obviously intended to maximize the quantity and quality of agricultural production, but the side effects that such products may have on soil microorganisms are often overlooked.

As summarized by Bünemann et al. , mineral fertilizers tend to have limited direct effects on soil microbiota. Indirectly, however, by improving crop productivity, yields and the amount of crop residues that remain in the soil, they can influence its microbial communities.

Nitrogen fertilization can acidify soil pH, with potential negative effects on the microorganisms present. Organic amendments are both a direct source of carbon and an indirect source of this element for the microbiota, always in terms of crop yield and crop residues. However, the quality of the organic waste matrices with which soil amendments and fertilizers can be produced must be controlled (think of the case of MSW composts), to avoid the accumulation of toxic substances in the soil.

Herbicides, fungicides and insecticides can have different effects on soil microorganisms: suffice it to mention the case of copper which, due to its potential toxic effect on microorganisms, can be used in the European Union but with dosage restrictions.

The organic matter added to cultivated soils for the purpose of improving their physical and chemical fertility is well-known to also affect biological fertility, interacting with the entire population of microorganisms present in the soil, both with beneficial and harmful ones (pathogens and parasites).

Therefore, to maximize the effectiveness of adding organic matter to cultivated soils, it’s essential to adequately understand these interactions and how they are influenced by other agricultural practices, such as tillage used to bury soil amendments and fertilizers.

The research conducted on the burial of organic matter leads to variable results. For example, it can cause a reduction in fungal biomass and cause even very important alterations in the populations of nematodes and protozoa in the most superficial layers of the soil, while bacteria are much less sensitive to this farming practice. However, as we have already described in this article, it’s important to emphasize that even the microfauna and the microflora of deeper layers of the soil play a decisive role in the cycles of the nutrients. And the effects of the burial of organic matter on the microbiota of these horizons are still poorly studied.

In addition to analyzing the effects of individual farming practices on the texture and composition of soil microbial communities, it is possible to consider combinations of techniques.

A ten-year research conducted in Zurich starting in 2009 on wheat, which has been given the name FAST (FarmingSystems and Tillage), collected data in two replicates placed next to each other on the same plot, in order to minimize the variations caused by the spatial heterogeneity of the soil. The experiment was designed to compare conventional (C) and biological (O) management combined with different tillage regimes: intensive (IT), reduced (RT) and none (NT).

The conventional plots received synthetic mineral fertilizers, herbicides, insecticides and fungicides and were subjected to intensive processing (IT) and no processing (NT, with additional use of glyphosate). The corresponding culture systems have been named conventional with intensive tillage (C-IT) and conventional without tillage (C-NT).

The organic plots were fertilized with bovine slurry, they did not receive synthetic pesticides and were subjected to intensive (IT) or reduced (RT) processing, giving rise to the farming systems called organic with intensive processing (O-IT) and organic with reduced processing (O-RT).

The effects of the different combinations of cropping system and processing intensity were measured on the microbiota of the soil of the plot, and on that of the rhizosphere of wheat plants.

The results demonstrated that soil bacterial communities are primarily affected by tillage, while fungal communities vary primarily in response to the type of management, and only secondarily in response to tillage. At the rhizosphere level, however, the type of management is the factor that has most influenced bacteria, while fungi have generally been influenced by variations in the intensity of tillage. Therefore, the adoption of certain farming techniques has different effects on the microbiota of the two portions of soil.

While analyzing in more detail the weight of the influence of agronomic techniques on the composition of microbial populations, it was revealed that about 10% of the variation in communities of soil microorganisms is explained by tested farming practices. The microbes most sensitive to farming techniques are taxonomically diverse and also include the so-called ‘frequent members’ of communities or the so-called ‘co-occurring members’, suggesting that farming practices may make it possible to address the presence or absence of these species. Microbes that frequently co-occur with many others are referred to as ‘key taxa‘, because they can play an ecologically important role, determining community dynamics and the functioning of the microbiota.

The members of the soil and root microbiota interact directly and indirectly with each other, and one tool to better understand these potential interactions is the analysis of co-occurrence networks. Long used in the social sciences to analyze relationships between human beings, network analyses have recently been applied to soil microbial ecology, to define the models based on which microbial communities assemble, as well as the response patterns of different taxonomic groups to agronomic techniques, and to identify the individual members of the microbiota that significantly influence the composition of the community.

Conventionally and biologically managed soils have been shown to host distinct microbial networks, but it is not clear whether the key taxa of soil and root microbiota are sensitive to farming practices.

Studying and understanding the way in which farming techniques, even combined with each other, are able to modify soil microbial communities, and in particular their “key taxa”, is essential to be able to direct their composition so that it benefits the best nutritional and phytosanitary status of plant crops, with the goal of smart farming.