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Soil Biota in Orchards

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Soil Biota in Orchards

Written by: Tianna Dupont, WSU Tree FRuit Extension. posted: October 2018.


The soil is alive. In just one acre of agricultural soil there can be 5,000 pounds of bacteria and fungi, 800 pounds of arthropods, 300 pounds of protozoa and 100 pounds of nematodes (Kounang, Pimentel, and Kounang 1998). These organisms provide many ecosystem services that are essential for the healthy growth of your trees. For example, soil biota suppress pests; mineralize, scavenge and cycle nutrients; and decompose plant and animal material, all ecosystem services which benefit orchard productivity.

Orchard floor management can increase the abundance and activity of soil biological communities. Organic matter additions from cover crops, crop residues, compost and other material feed the soil food web. Practices such as mulching tree rows with wood chips or mown and blown cover crops as well as compost applications have been seen to increase soil biota in orchards and the ecosystem services they provide.


Bacteria are the smallest but most numerous organisms in soil.  Bacteria are tiny, one-celled organisms, generally 4/100,000th of an inch wide (1 µm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. A teaspoon of productive soil generally contains between 100 million and one billion bacteria. That is as much mass as two cows per acre.

Bacteria fall into four main groups. Most are decomposers that consume things like root exudates and litter and help to break them down. As they consume nutrients moving into soil they hold them in their bodies and help “immobilize” nutrients like nitrogen so that they do not go out of the root zone. Another group of bacteria is called mutualists because they work with plants or other organisms in partnerships, such as those in plant roots that fix nitrogen. Others are plant pathogens and the last group is called lithotrophs and they use inorganic materials (such as sulfur and nitrogen) for their energy source instead of carbon. These play an important role in nutrient cycling.

Examples of ecosystem services provided by bacteria

Microbial Antagonism: Some bacteria excrete antibiotics. High populations of these bacteria in the root zone can help reduce infection by pathogens. Antibiotics are common among Streptomyces, and numerous strains of MicromonesporaandNocardiaare also active.


Fungi are composed of microscopic cells that usually grow as threads or strands called hyphae, which push their way between soil particles, rocks and roots. A single hypha can stretch from a few inches to a few miles.

Examples of ecosystem services provided by fungi:

Nutrient scavenging: One important group of fungi are called mycorrhizae. In particular are vesicular arbuscular mycorrhizae (a type of mycorrhizae where the fungi penetrate the cortical cells of the roots). They form a relationship with plant roots where the plant gives the fungi food (carbon) and the mycorrhizae scavenge for phosphorus, nitrogen, micronutrients and water. Hyphae are much thinner than roots and can reach areas the roots cannot. Mycorrhizae in orchards are not well studied but may be important in phosphorus limited soils (note phosphorus limitation is not common in Washington orchards). In one study Gąstoł, Domagała-Świątkiewicz, and Bijak (2016)found apple plants with arbuscular mycorrhizal associations had higher nitrogen, potassium, phosphorus and boron in shoots and nitrogen, sulfur, copper and iron in roots than plants without.

Pest suppression: Orchard soils higher in Trichoderma fungi (as well as Streptomyces and Pseudomonasbacteria) have been found to be more suppressive to the pathogens involved in replant disease than soils with lower levels of beneficials (Weerakoon et al. 2012). Abundant vesicular arbuscular mycorrhizae have also been found to successfully increase resistance to soil borne disease resulting in more shoot growth in one study in an apple replant situation (Taube-Baab and Baltrushat 1993).

Decomposition: Fungi are particularly good at breaking down complex substrates such as wood because they exude compounds such as ligninasethat chemically break down cell walls.


Protozoa are single celled organisms. They often have a small tail that motors them around in the soil solution. They are very predominant in forest soils, but also abundant in agricultural soils.

Ecosystem services provided by protozoa:

Nutrient cycling: Protozoa are important nutrient cyclers providing nitrogen in plant available forms as they consume bacteria in the soil (Griffith 1994). Protozoa have also been shown to enhance plant growth through mechanisms not related to nutrients such as stimulation of plant hormones (Bonkowski 2000, 2001). In one study of orchard soils in British Columbia, Canada protozoa numbered between 72 and 270 thousand per gram of soil (Forge 2003). Numbers were higher in treatments with large carbon inputs.


Micrograph of nematode.
Fig. 1. Bacterial feeding nematode (Panagrolaimus sp.) from Washington orchard soil. Photo credit: Tianna Dupont, WSU.

Nematodes are non-segmented cylindrical round worms. Nematodes are one of the most numerous organisms in the world, often exceeding millions per square meter. While nematodes inhabit a wide range of environments including marine and freshwater, in agricultural systems we are most interested in the microscopic nematodes which inhabit the water films in soil. Fungal feeding and bacterial feeding, predatory and omnivorous nematodes provide a number of services including nitrogen mineralization and plant pathogen suppression. In a current study in Washington, orchard soils averaged 800 million nematodes per acre in the top six inches (DuPont and Kalcsits, unpublished)1.

Ecosytem functions of nematodes:

Nitrogen mineralization:Bacterial and fungal feeding nematodes are important because like protozoa when they eat bacteria and fungi they excrete nitrogen in a plant available form (ammonia) (Figure 1). Predators and omnivores also release nitrogen as they consume other organisms. In grasslands nematodes can mineralize as much as 8-22% of available nitrogen (Elliott, Hunt, and Walter 1988), 28 lbs/acre/year in one study (Culman et al. 2010). In orchards, one study found nitrogen fluctuations of 97 to 617 mg N per kg soil per year by bacterial/fungal feeding nematodes and protozoa (Forge 2003). One way to measure the nutrient cycling potential of soil is by looking at the proportion of bacterial and fungal feeding nematodes compared to other nematodes in the soil. This measurement is called the Enrichment Index (EI).

Micrograph of a root lesions nematode.
Fig. 2. Lesion nematode (Pratylenchus sp.) from Washington Orchard soil. Photo credit: Tianna DuPont, WSU.

Plant parasitism:In orchards lesion nematode (Pratylenchus) (Figure 2), dagger nematode (Xiphenema), and ring nematode (Criconema) can cause economic damage. Lesion nematode is known to be part of the replant complex. It can directly impact root growth and nutrient uptake by disrupting cells as it feeds as well as provide an entry point for other fungi and bacteria to infect tree roots. Dagger nematode can vector Tobacco ringspot virus causing apple union necrosis and apple decline as well as Cherry rasp leaf virus,which causes rasp leaf disease, strains of Tomato ringspot virus,which cause yellow bud mosaic, cherry mottle leaf, and Prunus stem pitting diseases.

Pest Suppression:Nematodes can also indicate the structure and complexity of soil food webs. Soils with a larger proportion of omnivore and predator nematodes tend to have larger amounts of other beneficial organisms as well and they provide pest suppression and soil food web stability. In one study of apple in British Columbia, certain mulch treatments led to larger proportions of the omnivore/predator nematodes and also to significantly lower levels of root lesion nematode (Forge et al. 2003). Some nematodes will attack insects (e.g., Steinernema) and may be useful in pest management where a part of the life cycle is in the soil, as with overwintering codling moth larvae (Lacey et al. 2006).

Micrograph of a collembola.
Fig. 3 Collembola (Sminthuridae). Photo credit: Ashton Hansen and Deirdre Prischmann-Voldseth.


Soil microarthropods are abundant small invertebrates that live in the soil and litter layer. Typical microarthropods include mites, springtails, pseudoscorpions, and insect larvae. These microarthropods can be important in controlling the rate of litter decomposition and altering nutrient cycling. In a current study mites and collembolans counted in the top four inches of orchard soil ranged from 0 to 25,000 per meter square (DuPont and Kalcsits, unpublished).


Collembola or “springtails” live in the litter and soil pores in the upper four inches of the soil (Figure 3). They feed mainly on fungi, bacteria, and algae growing on decomposing plant litter. Only a few millimeters in length they are able to escape danger by “springing” high into the air with a forked tail-like furcula.

Micrograph of two species of Oribatid mites.
Fig. 4 Oribatida mites SEM. Photo credit: Sarah Hewitt and Deirdre Prischmann-Voldseth.

Fungal Feeding and Predator Mites

Soil mites such as Oribatids(Figure 4) eat fungi, algae, and dead plant material. These mites are extremely important. They break down dead leaves and other material returning nutrients to the soil. Predator mites such as Mesostigmata (Figure 5) suppress pests and mineralize nutrients as they eat their prey.

Ecosystem services provided by microarthropods:

N mineralization: Mesofauna feeding on microbes excrete nitrogen-rich waste contributing up to 30% of mineralized N (Deruiter et al. 1993; Griffiths 1994), and increasing plant uptake up to 50% (Laakso, Setala, and Palojarvi 2000).

Pest suppression: Predation by Mesostigmata and other predacious mites can help keep pests in check.

Micrograph of a mesostigmata mite.
Fig. 5. Mesostigmata mite (Geolaelaps sp.). Photo credit: Eric Knutson and Deirdre Prischmann-Voldseth.


Ground beetles (Carabidae) (Figure 6) and Rove beetles (Staphylinidae) are highly mobile generalist predators found in the leaf litter. Carabids in orchards can be highly diverse with 30 to 60 species. (Cross et al. 2015).

Ecosystem services provided by macroarthropods:

Pest suppression: Codling moth, oriental fruit moth, apple maggot fly, apple leaf midge, plum curculio, wooly apply aphid, cherry fruit fly, and others spend part of their life cycle in the soil or leaf litter where they can be attacked by beetles and spiders. A number of studies have shown significant predation of codling moth by carabid beetles (de Roince et al. 2012; Hagley and Allen 1988). For example, in a small study, 34–81% of fourth and fifth-instar codling moth larvae were attacked by beetles and other predators on the ground of an apple orchard (Mathews, Bottrell, and Brown 2004). Spiders, such as wolf spiders are also active predators.

Micrograph of a carabid beetle.
Fig. 6. A Carabid beetle (Carabidae). Photo credit: Sarah Hewitt and Deirdre Prischmann-Voldseth.


In order to increase the ecosystem services provided by soil biota in orchards we can manage the orchard floor: providing food resources and limiting disturbance.

Feed the soil: Adding organic matter to soil is essential to promote active abundant soil biological communities. Cover crops, leaves, compost, prunings, manure, wood chips – all these organic materials that we add to soil are the food for these organisms (Caigelli 2012, Janvier 2007). Which type of organic material we add to soil changes which type of organisms will have the largest numbers. For example, adding material very high in carbon will encourage fungi who excrete enzymes such as chitinase which can break down tough to digest material.

Manage disturbances: Some soil perturbations are a normal part of soil processes or are a necessary part of agriculture and other land uses. However, some disturbances significantly impact soil biology and can be minimized to reduce their negative effects. Tillage is a particularly important disturbance affecting soil biology. For example, surface tillage may destroy tree feeder roots and beneficial fungal hyphae.

Compaction: Ideally, soils are approximately 50 to 60% pore space comprising a variety of pore sizes and lengths. The size and continuity of pores controls whether larger microbes, such as protozoa, can prey upon bacteria and fungi. Compaction reduces the diversity of pore sizes and the amount of space and pathways available for larger organisms (figure 2) to move through the soil. This favors bacteria and small predators over fungi and the larger predators.

Arthropods are severely affected by compaction. Among nematodes, the predatory species are most sensitive to compaction, followed by fungal-feeders, then bacterial-feeders. Root-feeding nematodes are least sensitive to compaction—perhaps because they do not need to move through soil in search of food. Compaction changes the movement of air and water through soil, can cause a shift from aerobic to more anaerobic organisms, and may increase losses of nitrogen to the atmosphere (denitrification). Rooting depth may be limited in highly compacted soils. Compaction restricts the depth of the rhizosphere environment that supports microbes.

Pesticides: There is some literature showing negative impacts of pesticides on soil biota such as micro-arthropods (Doles, Zimmerman, and Moore 2001; Brown and Adler 1989; Brown and Puterka 1997). However, this relationship can be complicated with some pesticides such as herbicides providing a flush of microbial growth in response to readily available resources. Declines in soil biota in orchard soils with continual herbicide use (Yao et al. 2005) is more likely due to the lack of carbon inputs into the soil than toxic effects of the herbicides themselves.

Other: Orchard floor management can affect soil biology. Keeping the soil covered and with living roots for much of the year also generally encourage soil biology both from habitat (lessening environmental extremes) and food source (root exudates, dead roots, plant litter). Plastic mulch negatively affected carabid beetle numbers (Mathews, Bottrell, and Brown 2004) and soil microbes (Forge et al. 2003) in two orchard floor studies.


There are many indicators of soil biological function. We will describe a few here.
Soil Protein Index is an indicator of the fraction of soil organic matter that is present as proteins. This organically bound nitrogen can be mineralized by soil biota and become available for plant uptake. It is an indicator of the soil’s ability to store N and is associated with microbial activity as well as aggregate stability.

Soil Respiration is a measure of the metabolic activity of the soil microbial community. There are a number of protocols for measuring soil respiration. Cornell quantifies CO2 released from re-wetted soil held in an airtight jar for 4 days. However, respiration can change rapidly (e.g., from dry to wet soil, with a management intervention like compost) and thus it may be difficult to interpret the results with confidence.
Active Carbon is the portion of the soil organic carbon that is readily available as a food source for microbes. It is generally directly related to the size and activity of the microbial community, yet its level does not vary as quickly as the microbial biomass. It is measured by a reaction with permanganate.

Nematode analysis is done by washing nematodes from soil and using Baerman funnels and centrifugation to concentrate nematodes in water where they are counted under the microscope.


1Average of 79 nematodes per 100 grams of dry soil from apple orchards, including bacterial feeding, fungal feeding, plant parasitic, predacious and omnivore nematodes. Assuming 2,000,000 lbs (1,000 tons) of soil in the top six inches of an acre (Dupont and Kalkcits, unpublished data).


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