SOIL ORGANISMS
This section focuses on describing the different organisms. For more detail on their functional role in the soil, see the Soil Ecology Section
Soil Organism Categories by Size and Type
NB: there is some discussion over the exact boundaries of these categories, but these are taken from the UNFAO State of Knowledge of Soil Biodiversity Report 2020.
| Size Category | Body/ Organism Size | Organism Types |
|---|---|---|
| Microbes | Up to 10 μm | Virus, bacteria, Archaea, fungi |
| Microfauna | 10µm* – 0.1mm | All Protozoa, soil nematodes, rotifers, tardigrades |
| Mesofauna | 0.1mm – 2mm | Mainly microarthropods such as acari (mites) and collembola (springtails), small spiders, enchytraeids (tiny worms), insect larvae, small isopods (woodlice types) and small myriapods (centipedes and millipedes). |
| Macrofauna | 2mm- 20 mm | certain earthworms, gastropods, isopods, myriapods, ants, some spiders and the majority of insects. |
| Megafauna | 20 mm | large size invertebrates (earthworms, snails, myriapods) and vertebrates (insectivores, small rodents, reptiles and amphibians) |
Sources: Menta, C. 2012 and State of Knowledge of Soil Biodiversity, 2020
Who’s who, and who eats who?
Much of this section has been extracted from the 2016 Global Soil Biodiversity Atlas with grateful thanks to this work.
(see references below)
1. Soil microbes : Virus, bacteria, Archaea, fungi
This is an extremely diverse group which regulate key chemical weathering and decomposition processes for ecosystem functioning that are essential for ecosystem health and resilience. The biomass from this group represents 1 to 4 % of total soil carbon (up to three tonnes of carbon per hectare).
They mostly rely on the supply of carbon compounds for energy, and in the process they regulate the decomposition and stabilisation of soil organic matter and largely contribute to nutrient cycling. Many soil micro-organisms are tightly associated with (living) plants and have enormous effect on plant health. Conditions in the soil (e.g. pH, temperature, oxygen) will determine the species and quantities present and the positive or negative influence on plant health. For example, a 30-fold decrease in bacterial biomass was found when comparing high to low pH soils.
Viruses – The abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands and is strongly influenced by water availability and temperature. Relatively little is really known about this group of soil organisms, with most of the focus on crop or livestock pathogen viruses, with soil viral diversity severely underestimated and under-sampled. Most information on viruses covers the disease causing organisms, particularly those that impact human, livestock or crop health.
Bacteria and archaea These single celled eukaryotes (no nucleus or internal organelles) play a vital rolein creating, maintenance and functioning of soil, as discussed in the Soil Ecology Section. Their reliance on carbon sources results in four major functional groups:
Saprotrophs (decomposers): living on dead organic material and contributing to carbon and nutrient cycling and formation of stable soil organic matter (humus). When nutrients are limited, they also immobilize nutrients in their cells and then can reduce plant growth.
Mutualistic symbiosis: Form beneficial symbioses with plants, like the nitrogen- fixing bacteria that occur on the root nodules of certain plants (rhizobium).
Commensal symbiosis: is a class of relationship between two organisms where one organism benefits from the other without affecting it.
Pathogenic symbiosis: Cause disease and potentially death in living organisms. Some cause plant diseases, but others may also help control and balance plant pests and diseases.
An additional group of bacteria are the chemoautotrophs, which obtain energy from nitrogen, sulphur, iron, or hydrogen instead of carbon compounds. Some of these species are important for nitrogen cycling and degradation of pollutants.
Nitrogen Fixing bacteria are significant in agricultural settings. Azotobacter: Large-scale agricultural application of this organism has been used in Russia and in India, and several commercial inocula of wild-type Azotobacter are currently being marketed in the UK. Azotobacter is one of the few nitrogen-fixing organisms that fixes it aerobically. It also fixes nitrogen more rapidly than most of the other bacteria. Azotobacter can utilise a wide variety of carbon and energy sources, such as sugars, alcohols, fatty acids, starch, and alkanes. These compounds are common industrial waste products. The organism forms cysts that prevent it from dying during times of nutrient deprivation or desiccation. Plant-growth hormones are also released from Azotobacter making it an attractive group for agricultural applications.
Actinomycete bacteria are worth a special mention here although their numbers are generally one to two orders of magnitude smaller than the total bacterial population. They are an important component of the bacterial community, especially under conditions of high pH, high temperature or water stress. They appear very similar to fungi with very thin (approx. 1/1000th mm) mycelial threads, hence, are much thinner and occupy a different ecological niche. Mostly found in aerobic soil, they are of huge economic importance because they are very abundant and are key for soil carbon cycling, notably recalcitrant plant and insect polymers like chitin, lignin, cellulose and hemicellulose. In addition, actinomycete bacteria synthesise and excrete thousands of metabolites into soil, including (for example, Streptomycetes) antibiotics that kill or inhibit the growth of plant pathogens, providing a healthy environment for plant growth. The wider phylum of Actinomycete bacteria also includes the nitrogen-fixing bacteria of the genus Frankia. The earthy smell after it rains is linked to geosmin produced by actinomycete bacteria.
Actinomycetes
• Capable of degradation of complex organic molecules
• Capable of biological nitrogen fixation with species of the non-legume-associated Frankia
Characteristics and Functions of Actinomycetes
| Characteristics | |
|---|---|
| Structure | Prokaryotic |
| Size | 1-2μm diameter |
| Morphology | Filamentous lengths of cocci |
| Gram stain | Gram positive |
| Respiration | Mostly aerobic, can be anaerobic |
| Habitat | Soil or marine |
| Abundance, marine isolates | 5-40 CFU/ml |
| Abundance, soils | 106-108/g |
Protozoans: Protozoa are single-celled eukaryotes (i.e. contain a nucleus and other organelles within the cell). Soil protozoa typically have a contractile vacuole (internal sac) for regulating water and ion concentrations, and they will form cysts in sub-optimum living conditions or when prey are scarce. Other groups feed on bacteria or fungal hyphae, or parasitise soil invertebrates. Relatively little is understood about many of these organisms, which include:
Ameobozoa (amoeba and slime molds): which live on moist surfaces feeding on mostly bacteria, although a small number feed on fungal hyphae or prey on other protists or microinvertebrates. There can be as many as 100,000 cells/g of soil, but more typically numbers are 103 -104 cells/g.
Rhizaria: The most common active protists in soils are cercozoa, small bacterial-feeding unicells less than 10 µm in size, but others feed on fungal hyphae, plants or soil invertebrates. Abundances vary with moisture as well as with the abundance of bacteria or other prey. Densities may reach more than one million cells/g of soil but are usually 103 -105 cells/g.
Alveolata: characterised by folded membranes, the ciliates (with beating cilia for mobility) are the only free-living soil dwelling members of this group. Most species have rows of cilia that beat in a coordinated manner, and a specialised funnel structure for capturing and ingesting prey. They also often have specific defensive or aggressive structures, called ejectosomes. Most ciliates ingest bacteria, but some ingest other protists, dead invertebrates or are specialised symbionts or parasites. Two other groups are the Colpodid to Hypotrich and the ratio of these (also called the Colpodid to Stichotrich ratio) is used as an indicator of environmental quality. There can be 10,000 active cells/g declining to none in very dry soils. Although the biomass of ciliates per gramme of soil is very low, when active they can ingest several hundred bacterial cells per minute.
Examples of Marine ciliates
Morphology of ciliate species in vivo. (A) Pseudokeronopsis carnea; (B) Diophrys scutum; (C) Urceolaria urechi; (D) Hemigastrostyla elongata; (E) Pseudokeronopsis flava; (F) Paramecium aurelia; (G) Uroleptopsis citrina; (H) Condylostoma spathiosum; (I) Cardiostomatella sp.; (J) Boveria labialis; (K) Coleps sp.; (L) Strombidium sulcatum. Scale bars = 50 μm.
Stramenopiles: Includes brown algae, hyphochytriales and peronosporomycetes, which are commonly found in soils. They absorb nutrients from the living or decomposing tissues into which they grow. They are economically important because they include species that cause some of the most damaging plant diseases, such as Pythium (which causes the damping-off disease in greenhouses), downy mildews and white blister rusts. Oomycetes, also known as water moulds, comes under this group. It includes several plant pathogens including Phytophthora infestans, which caused the potato blight of the Irish Potato Famine. https://www.slideserve.com/hasad-dean/stramenopiles
Diatoms consist of several genera of unicellular microalgae, which live individually or as colonies and are some of the most stunning forms and colours to be seen in nature, they are a pleasure to observe, especially the gliding types. They primarily exist in wet environments and generate up to 50% of the oxygen produced on earth and absorb nearly 7 billion tons of silicon each year.
Soil fungi exist primarily as a mass of multicellular threads of hyphae known as mycelium. They fall into the same three functional groups as bacteria/archae above. The mutualists group include the recently much-heralded mycorrhizal fungi, which consume plant root exudates (secreted carbon compounds) in exchange for supplying minerals to the plant. The nutrient/mineral exchanges between fungi, bacteria and plants are absolutely critical for a self-sustaining, healthy, soil system.
Together with bacteria, fungal hyphae constitute the largest portion of the microbial biomass of soil. The balance of bacteria to fungi shifts with habitat succession from disturbed soils (bacteria dominant) through to mature forests (fungi dominant). Disturbed, bacteria-dominated, systems can lack the nutrient cycling to support healthy, aerated systems for crops and pasture, especially if the soil is waterlogged or lacking porous structures.
Fungi in soilsconsists of two main phyla: Ascomycota, usually with a cup-like or disc-like fruiting body, and Basidiomycota, usually with an umbrella shaped cap borne on a stalk. This category also contains soil fungus from the Glomeromycota, Zygomycota, Chytridiomycota and Blastocladiomycota phyla.
Mycorrhizal fungi can be categorised as follows:
Endomycorrhizal fungi includes several groups of fungi that penetrate into the cells of roots, working in symbiotic nutrient exchange. Glomeromycota: form arbuscular mycorrhizal (‘fungus-root’) symbioses and produce abundant hyphae and spores in soils. In grasslands and agricultural lands, these fungi comprise an estimated 20-30 % of soil microbial biomass, making arbuscular mycorrhizal fungi among the most abundant organisms in many soils.
Ectomycorrhizal fungihave hyphae that weave between cells in plant roots. These associate with trees and may contribute up to 33% of all forest soil microbial biomass. This group contains many of the best edible fungi.
Ectendomycorrhizal fungi exhibit features from both the above categories, and associate with pine, spruce and larch species.
Fungi can play a role in balancing the impact of pests on crops. Some entomopathogenic fungi will infect and kill certain pests such as pea moth, aphids, wireworms, pollen beetles, bean seed flies and moth larvae and cutworms.
2. Microfauna and mesofauna
Of the micro-arthropods, springtails (Collembola) and mites (Acari) play a primary role in the recycling of nutrients within terrestrial ecosystems. They stimulate microbial activity and contribute to the mineralization of nitrogen and thereby to plant growth. As such they play an important role in soil fertility.
Collembola (springtails) represent one of the most important groups of soil microarthropods, both because of the number of species, and the number of individuals generally present in soils. They are very useful as indicators of soil quality as their biodiversity and density are influenced by numerous soil factors (mainly organic matter and water content but also other factors such as contamination).
Most springtails primarily graze on fungal hyphae and spores, but also consume pollen, algae, bacteria or decaying organic matter. Carnivorous species help balance populations of small invertebrates such as nematodes, rotifers, and even other collembolan species. They do not harm living plants. Typically, seeing springtails is a positive thing.
Acari (mites): oribatid mites (Oribatei) are the characteristic mites of the soil and are usually eat fungi or dead matter. Mesostigmatid mites are nearly all predators on other small fauna, although a few species arefungivores. They may become numerous at times and have even been observed eating their own young[TR2] . Astigmatid mites are associated with rich, decomposing nitrogen sources and are rare except in agricultural soils. The Prostigmata contains a broad diversity of mites with several feeding habits. Regarding soil mesofauna, mites make up a larger part of the group than any of the other soil animals. Mites are an integral part of the soil food web and mesofauna, as well as playing an important role in decomposition and soil fertility. In heavily disturbed ecosystems, such as cities or industrial areas, soil mites can be the last indicator of the original habitats. This suggests that it is possible to reconstruct the vegetation type and landscape conditions based on the mite communities remaining in degraded areas.
Enchyraeids (potworms), despite popular belief, are not plant parasites. Enchytraeids are concentrated in the top 5cm of soil where organic matter accumulates. Most studies regard them as microbial-feeders, frequently grazing on bacteria and fungal mycelia. They also feed on dead material or residues excreted from other organisms. There is also some weak evidence that some species eat nematodes. In old, wet, and organic-matter rich ecosystems with low pH, they replace earthworms and take over the role of ecosystem engineer, and these systems cannot function without them.
Protura and Diplurans: Proturas are closely related to springtails, and primarily eat fungal hyphae. Dipluras can look similar to earwigs with long antenae and bristle tails, and most dipluran feed on plant-material, but some consume nematodes.
Nematodes are microscopic worms that are hugely diverse and abundant: 1 kg of soil can comprise about 20,000 nematodes. Although the plant feeder species are often associated with reduced plant growth or plant diseases, the majority of terrestrial nematodes contribute to the recycling of nutrients and thereby to soil fertility. In addition, some nematodes will parasitise pests like pollen beetle, cutworms, pea and bean weavils.
| Nematodes can be classified into different feeding groups based on the structure of their mouthparts. (a) bacterial feeder (b) fungal feeder (c) plant feeder (d) predator (e) omnivore |
Tardigrades, or ‘water-bears’, are incredibly tough, withstanding periods of extreme drought and cold. They eat bacteria, plants, and other microscopic organisms. They require wet systems to be active, but can be found in the water films surrounding soil particles and in mosses. Their function is not fully known, but all tardigrades have stylets to pierce animal or plant cells, and a pumping pharynx to suck out their internal fluids, although some species are carnivorous and consume rotifers and nematodes.
Rotifers are microscopic animals that move by beating cilia on their heads and feed on bacteria or small algal cells. A few are predators of ciliates or of other rotifers, or suck out the content of cells after piercing the cell wall. Although they need water to live actively, the bdelloids, which are the most successful soil rotifers, have an extraordinary ability to survive prolonged periods of desiccation through a process called anhydrobiosis. Difficult to study, little is known of their role in the functioning of soil systems.
3. Macro and Megafauna
Earthworms are significant ecosystem engineers, driving many beneficial processes in the soil, as outlined in the tables in the Soil Ecology Section. Their abundance and types can also indicate soil quality and health. Earthworms are able to produce plant growth hormones and to modify the expression of plant genes. They may, for example, render a plant tolerant to plant-parasitic nematodes.
Epigeic species live at the soil surface and feed on plant residues and manure. They are small and uniformly coloured worms, pigmented green, blue or reddish.
Anecic species feed on surface litter that they mix with soil, and create deep vertical burrow, thus mixing horizontal soil layers. They are large worms with a dark pigmentation and strong anterior digging muscles.
Endogeic species are pale and seldom come to the soil surface and consume large amounts of soil from which they extract the lower levels of organic matter from these deeper layers. Density is often in the range of 100 to 500 individuals per square metre
Muriapods (centipedes, millipedes, pauropods, symphylans): 0.5 -385 mm animals with elongated segmented bodies and many legs, which live in soil, some digging burrows, preferring areas with high moisture, consistent temperature, and low levels of ultraviolet light. Centipedes are primarily predators. Symphylans are generally root-feeders. Pauropods eat fungi, and millipedes eat dead leaf litter. Symphylans and pauropods are distributed unevenly, and in lower abundance than milipedes since they are very responsive to changes in soil properties (chemical as well as physical) and food availability. Millipedes are important decomposers of leaf litter.They are estimated to break down 10-15% of the annual leaf fall and their significance for litter processing is higher than that of earthworms in boreal forests.
Ants: Ants are social insects and form nests in trees, on the soil surface and underground. Some ants eat plants, others prey on other insects, and others are considered ominvores. Ants
play an important role in the maintenance and functioning of soils, as they dig tunnels and chambers, thus promoting nutrient cycling through soil bioturbation (the reworking of soil) and water infiltration. They produce soil organic debris, thus enabling the processes of decomposition performed by fungi and bacteria and increasing the heterogeneity of the soil resource.
Woodlice (Isopods): Isopods can be as small as 1mm, and feed on dead leaf litter and contribute significantly to decomposition in many ecosystems through feeding on and digesting leaf litter, dispersing microbial spores and mediating microbial activity and nutrient cycles. In their gut, isopods can also develop symbiotic relationships with bacteria to help digest cellulose, and these can cause the isopod to change sex!
Beetles: Many beetles live on the soil surface or dig burrows into the soil and many Coleoptera larvae develop in soil. Numerous beetles (families Carabidae, Leiodidae, Staphylinidae and Scarabaeidae) are well adapted to the soil environment. Some carrion beetles (family Silphidae) and some dung beetles (family Scarabaeidae) build nests in the soil. Beetles play major roles in decomposition, including feeding on dead plants, dead animals, dung, and preying directly on other soil animals. Many ground beetles are voracious predators of small soil animals, including slugs and snails as well as earthworms, collembolans and nematodes. Staphylinid (rove) and carabid (ground) beetles have been shown to control frit fly in cereals, and carabids predate flea beetle eggs and pollen beetles. Ladybirds will overwinter under leaf litter or at the base of woody perennials such as fruit bushes, and have been shown to have beneficial predatory impacts on various crop pests. Others feed on fungi or dead wood. Beetles are the largest and most diverse order of organisms on the planet.
An information hub for farmers has been launched by farmers, vets and entomologists, describing the benefits of dung beetles for farmers and providing pragmatic prescriptive information for farmers to help dung beetles.
Insect larvae in soils: Diptera (true flies) larvae in general look like small worms as they are all legless. However, their ecological functions are very diverse. Some of them mine taproots and feed on the internal cortex, causing disease. Others live in litter or dung, which they decompose. Many are problematic for growers if numbers escalate i.e. are not controlled by predators. The majority of the lepidoptera (butterfly/moth) larvae feed on green plants. Coleoptera larvae are represented by hundreds of families with different feeding habits. Some longhorn beetle larvae (Cerambycidae) bore into roots or rhizomes. Click beetles larvae (wireworms) and scarabaeid larvae chew fine roots or decaying plants. Most Neuroptera larvae (like lacewings, alder flies) are useful predators, consuming aphids and insect eggs, with elongated mandibles. By using the mandibles, they catch and pierce prey, and inject digestive juices.
Other ground dwelling macrofauna: These organisms may have a high ecological importance (e.g. as decomposers of litter, and pest predators). Of these Arachnida (e.g. spiders), Gastropoda (e.g. snails and slugs) and some Hymenoptera (e.g. mining bees) are particularly notable:
Spiders mostly prey on insects and soil is often used as their hunting ground, in which they use different methods of capturing prey. Spiders will hunt various pests, such as wolf spiders consuming flea beetles, aphids, thrips (like thunderbugs) and moth pests like cutworm. Spiders have also been shown to help control frit fly in cereal crops, wolf spiders and theridion spiders predate on pollen beetles that attack brassica crops.
Slugs and snails are often considered pests in growing systems, however, along with earthworms, the mucous secretions, the faeces (especially those of earthworms) and the bodies themselves of the animals (when they die) influence in large measure the concentration of nutrients present in the soil particularly potassium, phosphorous and nitrogen, reducing the C/N ratio of the litter and facilitating decomposition. Snails are usually herbivorous; however, some species are carnivores. Most slugs feed on a broad spectrum of organic materials, including leaves from living plants, lichens, fungi and even carrion.
Mining bee burrows can reach 60 cm in depth. These solitary bees (specifically Colletes and Andrena, two common widespread genera) are good pollinators of economically important plants. They are often ‘oligolectic’, meaning that they collect pollen from only a select few plant species, and if that plant becomes rare or extinct, so does its pollinator.
Source: Soil microarthropod community in a beech forest of Northern Italy (Menta, C. 2012)
References AND USEFUL RESOURCES
- The Soil Biota, Wageningen University & Research, The Netherlands
- Chaos of Delight: mesofauna information and photography
- eOrganic, Oregon State University
- David C. Coleman, Chapter: Soil Biota, Soil Systems, and Processes, in Encyclopedia of Biodiversity, 2001
- Łukasz Gajda et al, Food preferences of enchytraeids 2017
- Cristina Menta (August 29th 2012). Soil Fauna Diversity – Function, Soil Degradation, Biological Indices, Soil Restoration, Biodiversity Conservation and Utilization in a Diverse World, Gbolagade Akeem Lameed, IntechOpen, DOI: 10.5772/51091. Available from: https://www.intechopen.com/books/biodiversity-conservation-and-utilization-in-a-diverse-world/soil-fauna-diversity-function-soil-degradation-biological-indices-soil-restoration (Open source)
- Soil Mesofauna, FSC training March 2013 by Dr Matthew Shepherd, Dr Felicity Crotty, Dr Peter Shaw and Pete Boardman
- Global Soil Biodiversity Initiative
- Global Soil Biodiversity Atlas. 2016. Orgiazzi, A., R.D. Bardgett, E. Barrios, V. Behan-Pelletier, M. J. I. Briones, J. L. Chotte, G. B. De Deyn, P. Eggleton, N. Fierer, T. Fraser, K. Hedlund, S. Jeffrey, N. C. Johnson, A. Jones, E. Kandeler, N. Kaneko, P. Lavelle, P. Lemanceau, L. Miko, L. Montanarella, F. M. de Souza Moreira, K. S. Ramirez, S. Scheu, B. K. Singh, J. Six, W. H. van der Putten, and D. H. Wall. European Commission, Publications Office of the European Union, Luxembourg. (intended to be shared and used!)
- Biological control of crop pests through the manipulation of the farm ecological infrastructure and modification of the tillage regime, Section 1