It’s alive! Numerous microorganisms are responsible for the structure and fertility of soil, which is so much more than a field of crops or dirt underneath one’s fingernails: It is home to a microscopic world teeming with bacteria, fungi, protists and viruses.
With an estimated one trillion species, there are more microbes on Earth than stars in the galaxy. The thin layer of material covering the earth's surface, commonly known as soil, is especially rich in microscopic organisms: Every teaspoon of soil is assumed to be home to 200 meters of fungal hyphae and one billion bacterial cells . Many of them actively break down and recycle nutrients and ensure that our ecosystems are resilient to environmental changes.
As with other ecosystems on Earth, it is important to understand the many types of organisms and their functions, conserve them and thus contribute to the protection of our environment. For this reason, the multidisciplinary field of soil ecology developed. Soil ecologists are interested in the interaction of soil organisms with their physical and chemical environments . They investigate the diversity of the seemingly invisible organisms that live in soil and try to find out more about their important roles in keeping our environment healthy.
Soil – also referred to as earth or dirt – consists of plant residues, microbial and animal remains and minerals. These components are stuck together by sugars, which are secreted by microorganisms themselves or by plant roots, and form aggregates. The spaces between these aggregates can become filled with water or air.
In this complex maze, insects and earthworms burrow, further changing the structure of the soil and leaving their waste behind as food for microorganisms. Long fungal hyphae stretch through the soil and provide highways for bacteria to move from one place to another to access food. The structure of the soil environment also provides protection from predators.
As conditions in soil can change quickly with weather patterns, seasons or even fluctuations throughout the day, soil is also a very challenging environment for microorganisms to survive.
Because soil is a difficult habitat to live, microbes have developed many different strategies for obtaining the energy they need to survive. Microorganisms decompose organic matter by producing enzymes that break down dead plant, animal, and microbial remains into their simplest components. This way they recycle nutrients and make them easily usable for other living microorganisms and plants. In addition to this, microorganisms in the soil take up greenhouse gases such as carbon dioxide (CO2), dinitrogen monoxide (N2O) or methane (CH4) or release them into the atmosphere. This makes them also important players in global warming.
In addition to the role of bacteria and fungi in carbon cycling, there is growing evidence that viruses are a vital, yet under-studied part of it. Some viruses live inside bacterial or protist cells and control the way carbon is recycled in soil environments. By lysing their host cells and causing their death or by using their own genes related to carbon cycling, tiny viruses can thus play important roles in the global carbon cycle . Discovering the diversity of bacteria, fungi, protists and viruses that live in soil will help us to better understand and protect the health of our ecosystems.
Soil is not only a highly dynamic and challenging habitat for microbes to live, but also a very complex environment for scientists to study. Given the porous structure of soil, its microbial composition can vary from centimeter to centimeter. The types of microorganisms found in a location at a particular time can also change rapidly, as microbes grow, reproduce, die and migrate from one place to another. On top of that, the enormous number of different microorganisms also requires many different methods to study them.
Soil ecology has a long history. Major advances have already been made towards our understanding of the organisms living there and the important roles they play. Much of what we know about microorganisms in soil has been discovered using the following experimental techniques:
Samples for DNA sequencing can be collected from soils from different ecosystems, ranging from rainforests to deserts and from farms to alpine mountain peaks. In a first step, the DNA of the samples – which usually contain millions of bacterial and fungal cells as well as viral particles – is extracted and prepared in the lab. The DNA sequence, i.e. the genetic code of the soil microbes contained therein is then analyzed by sequencing machines. The use of DNA sequencing has helped to discover a large number of new organisms and to decipher their important functions in environmental processes.
Studying the diversity of microorganisms is still a difficult and exciting venture for many scientists. Today, highly sophisticated microscopes and microscopy techniques are used to look at the growth and spatial patterns of microorganisms.
The use of these novel techniques has contributed to an increased knowledge about specific types of bacteria, fungi and viruses that live in soils. It has helped to get insight into important processes controlled by soil microorganisms and revealed microbial functions affected by environmental change. Understanding microorganisms in soil will be essential for protecting farmland to grow the food we need, and for predicting how ecosystems around the world will withstand climate change. Scientists have already made enormous progress into this direction, but there are still gigantic numbers of microbes waiting to be discovered and analyzed.
The soil below our feet may only seem like a bunch of dirt, but it is a dynamic microbial world with large impacts on the world above-ground.
This text is a guest contribution from Dr. Lauren Alteio from the Department of Microbiology and Ecosystem Science, University of Vienna
 FAO, ITPS, GSBI, CBD and EC. 2020. State of knowledge of soil biodiversity - Status, challenges and potentialities, Report 2020. Rome, FAO.
 Nichols D., Cahoon N., Trakhtenberg EM et al.: Use of Ichip for High-Throughput In Situ Cultivation of “Uncultivable” Microbial Species (2010). Applied and Environmental Microbiology Apr 2010, 76 (8) 2445-2450