Chapter 128 - Soil Biota, Soil Systems, and Processes

Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use. This article was originally published in the Encyclopedia of Biodiversity, second edition, the copy attached is provided by Elsevier for the author’s benefit and for the benefit of the author’s institution, for non-commercial research and educational use. This includes without limitation use in instruction at your institution, distribution to specific colleagues, and providing a copy to your institution’s administrator.

All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier’s permissions site at: http://www.elsevier.com/locate/permissionusematerial Coleman David C. (2013) Soil Biota, Soil Systems, and Processes. In: Levin S.A. (ed.) Encyclopedia of Biodiversity, second edition, Volume 6, pp. 580-589. Waltham, MA: Academic Press. © 2013 Elsevier Inc. All rights reserved.

Author's personal copy Soil Biota, Soil Systems, and Processes David C Coleman, University of Georgia, GA, USA r 2013 Elsevier Inc. All rights reserved.

Glossary Domains The major divisions of the biota on earth, namely: Bacteria, Archaea, and the Eucarya. Ecosystem engineers The concept whereby members of the macrofauna (e.g., termites and earthworms) are actually moving parts of the soil volume for their own uses (e.g., making macropores which permit flow of large amounts of water rapidly through the soil). Immobilization The process wherein nutrients are taken up or immobilized in litter and other organic detritus until later (usually weeks to months) in the decomposition process.

Soils as Components of Ecosystems Soil-Forming Factors Soils are an intriguing, relatively thin (often o1 m depth) zone of physical–chemical and biological weathering of the earth’s land surface. Soils are formed by an array of factors, namely climate, organisms, parent material, the extent of slope, and aspect (relief) operating over time (Figure 1). These factors affect major ecosystem processes, such as primary production, decomposition, and nutrient cycling, which lead to the development of ecosystem properties unique to that soil type, as a result of its previous history. For example, a deep loess soil in Iowa, with a very fertile and deep surface or ‘‘A’’ horizon, containing considerable amounts of organic matter, will be very different from an ‘‘A’’ horizon developed in the Nebraska sandhills, with much greater porosity and lower water retention due to the nature of the sandy surface material. As noted in the soil-forming factors diagram (Figure 1), the array of biota – namely microbiota, vegetation, and consumers (herbivores, carnivores, detritivores) – is influenced by the soil processes and in turn has an impact on the soil system.

Polyphasic Nature of Soils, Influence on the Biota Soils are perhaps the ultimate in interface media, located at the intersection of four principal entities: the atmosphere, biosphere, lithosphere, and pedosphere (Figure 2). Soils provide a wide range and variety of microhabitats, thus accommodating a very diverse biota. The microbes (bacteria and fungi) are found in numerous microsites, well–aerated or not; bacteria may thus respire either aerobically or anaerobically. There is an enormous amount of surface area (hundreds of m2 per gram of soil) on the soil particles, which range in size classes from clays (0.1–2 mm in diameter) to silts (2–50 mm diameter) and sands (0.05–2 mm diameter). Numerous microbes and micro and mesofauna (protozoa and nematodes) exist in water films on these particles and in or on the surfaces of microaggregates formed from the primary particles. In turn,

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Larger mesofauna and macrofauna Live in pores in portions of soil profiles. Microfauna Animals that have high turnover rates, and live in water films in soils. Small mesofauna, such as nematodes, are also water-film dwellers. Mineralization The availability of inorganic nutrients in the decomposition of organic detritus, occurring after the immobilization phase. Organizing centers Soils are the centers of history and activity in terrestrial ecosystems.

the more mobile fauna, from collembola and mites (larger mesofauna) to the macrofauna (earthworms, millipedes, ants, termites, and fossorial or earth-dwelling vertebrates), move through the macro and micropores in the soil. The macrofauna play a role in moving parts of the soil profile around and form many sorts of burrows and pores; they are often termed as ‘‘ecological engineers.’’

Soils as Organizing Centers in Ecosystems Soils may be viewed as the organizing centers for terrestrial ecosystems. Major functions such as ecosystem production, respiration, and nutrient recycling are controlled by the rates at which nutrients are released by decomposition in the soil and litter horizons and transported to the photosynthetic layers of the ecosystem. This is particularly true for less heavily managed, near-natural ecosystems, many of which occur on soils having relatively poor nutrient status. In these systems, mycorrhizas are often obligate partners in the obtaining of adequate nutrients for the growing plants. Mycorrhizas (literally ‘‘fungus roots’’) are efficient at extracting nutrients from both mineral and organic sources, enabling plants to thrive in habitats that are considered to be poor in nutrients. We need to be aware of these and other mutualistic associations between microorganisms and roots, such as rhizobia and actinorrhizas, various root-associated symbiotic bacteria that facilitate the nitrogen fixation process on which the entire ecosystem often depends. These associations have arisen in soils over an evolutionary time and are key to an understanding of the ecosystem function.

Major Soil Processes Decomposition: Immobilization and Mineralization A very large proportion (greater than 90%) of the terrestrial net primary production is returned to the soil as dead organic

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Controlling factors Parent material

Climate

Vegetation

Relief

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Forests

Grazing Species Nutrient input Fire

Cultivation Fallow Crop selection Residue management Nutrient inputs Water management Fire Harvest (removal)

Seeding and planting Site preparation Watershed management Fire Harvest

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Processes Energy inputs and transformations

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Radiation Preliminary production Decomposition Nutrient cycling Immobilization Mineralization Weathering Translocation Transport Erosion Gaseous Leaching Development of ecosystem properties Vegetation Consumers Soil Base status Texture Organic matter Phosphorus Sulfur Nitrogen Salinity

Figure 1 Soil-forming factors and processes, and the interaction over time. Reproduced from Coleman DC, Reid CPP, and Cole CV (1983) Biological strategies of nutrient cycling in soil systems. Advances in Ecological Research 13: 1–55; and Coleman DC, Crossley Jr. DA, and Hendrix PF (2004) Fundamentals of Soil Ecology. San Diego: Academic Press.

litter. This litter, consisting of leaves, roots, and wood from trees and organic residues from agricultural fields, is decomposed on or in the soil, and the nutrients contained within it are recycled for further use. The decomposition process drives complex food webs in the soil, with numerous interactions between the initial agents of decomposition, the bacteria and fungi, and the fauna which in turn feed on them. Decomposition is the catabolism of organic compounds in plant litter and other organic detritus. Decomposition is principally the result of microbial activities; few soil animals have cellulases in their guts, which allow them to hydrolyze the celluloses in plant residues. The decomposition of organic residues involves the activities of a variety of soil biota, including both microbes and fauna, which interact conjointly in the process. For example, the initial breaking up of plant litter usually is conducted by the chewing and macerating action of

both large and small animals. This initial breaking into smaller pieces, or ‘‘comminution,’’ is a process that benefits the fauna, which derive nutritional benefit from the litter or microbes initially colonizing the plant material. The increased surface area and further inoculation of the smaller pieces enhances the microbial access to, and breakdown of, these tissues.

Nitrogen Cycle: Major Processes Nitrogen enters the ecosystem via nitrogen fixation, in which the dinitrogen molecule (N2) is separated into two nitrogen atoms, with considerable expenditure of energy and the assistance of the nitrogenase enzyme, to break the triple covalent bond. The atoms are ammonified and then used in the production of amino acids and proteins in the plants. Another

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avenue for nitrogen entry into the soils is by lightning fixation, in which the extensive high-voltage energy in the lightning charge ruptures the dinitrogen molecule, hydrogens are attached, and then the ammonium is brought in by rainfall. As shown in Figure 3, nitrogen is lost from the system via harvest and erosion of organic forms of N, it can be ammonified in decomposition, and then undergoes nitrification to nitrate

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(NO3 ), after which it can be taken up by biota, either through plant roots or into microbial tissues. If there is adequate energy and low amounts of oxygen present, there can be denitrification, in which the nitrogen is lost as either nitrogen gas (N2) or nitrous oxide (N2O). For further details, consult textbooks on ecology or ecosystem studies. The nitrogen cycle is of critical importance to biodiversity considerations, because key points in the cycle are dependent on the relatively species-poor assemblages of microbes, including the nitrogen fixation and nitrification steps. There are only a few species of nitrogen-fixing rhizobia, in the genera Rhizobium and Bradyrhizobium. The other principal nitrogenfixing symbiont, the bacterium Frankia (Actinomycetaceae) forming the actinorrhiza (literally actinomycete-root), contains only a few species in the genus. However, approximately 194 plant species in eight families and four different subclasses of flowering plants have been identified as hosts. These plants share the general tendency to grow in marginal soils and play an important role as pioneer species in early successional habitats. In the nitrification steps, noted in the previous paragraph there are only a few genera and species of nitrifiers. Most of them are autotrophic and quite sensitive to changes in soil pH. This means that these organisms may be unusually prone to getting diminished or eliminated in regions where there is considerable acid rain.

Biodiversity in Soils Figure 2 The pedosphere showing interactions of abiotic and biotic entities in the soil matrix. Reproduced from FitzPatrick EA (1984) Micromorphology of Soils. London: Chapman and Hall; and Coleman DC, Crossley Jr. DA, and Hendrix PF (2004) Fundamentals of Soil Ecology. San Diego: Academic Press.

Evolutionary History Soils as we know them, with well-differentiated profiles, probably developed concurrently with the origin of a land

N fixation

Streamwater losses

(1) Harvest and erosion losses

Biotic uptake N2 N2O Dentrification losses

Organic N

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NO3–

NH4+ Atmospheric deposition

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Figure 3 Inputs and outputs of N, which make up the intersystem transfers in an ecosystem. Numbers indicate groups of organisms active at a given stage of the N cycle. (1) Rhizobia, Frankia, (2) ammonifiers, (3) nitrifying bacteria, and (4) denitrifying bacteria. Denitrifying bacteria must compete with the biotic uptake of NO3 by other microbes and plants; thus the rate of nitrification sets an upper limit on denitrification losses. Stream water losses represent the excess of available N over that taken up by biotic processes. Modified from Waring RH and Schlesinger WH (1985) Forest Ecosystems. Orlando, FL: Academic Press.


flora in the early Devonian era, about 450 million years ago. The microorganisms that inhabit the soils, particularly the prokaryotic microbes such as the cyanobacteria, originated perhaps 3 billion years ago.

Diversity of Biota Biodiversity is an inclusive concept, which encompasses a wide range of functional attributes in ecosystems in addition to being concerned with the numbers of species present in the system. This differentiates it from the concept of species diversity, which is concerned with the identity and distribution of species in a given habitat or region. Soil biodiversity is best considered by focusing on the groups of soil organisms that play key roles in ecosystem functioning. Spheres of influence (SOI) (Coleman, 2008) of soil biota are recognized, such as the root biota, the shredders of organic matter, and the soil bioturbators. These organisms influence or control ecosystem processes, and exert further influence via their interactions with key soil biota (e.g., plants). What is the extent of redundancy within the functional groups of these SOI? Some soil organisms, such as the fungus and litter consuming microarthropods, are very speciose. For example, there are up to 170 species in one order of mites, Oribatida (members of the Arachnida, eight-legged arthropods), in the forest floor of one watershed in western North Carolina. In the soil biota, some of the species-poor functional groups, such as specialized bacteria, that is, nitrifiers and nitrogen fixers (Figure 3) are considered, at present, to be at most risk. Others include fungi forming mycorrhiza, a symbiotic association that benefits both plant and fungus, with the plant supplying high-quality carbon to the fungus, and the fungal hyphae exploring a greater volume of the soil, obtaining scarce mineral nutrients, particularly phosphorus. Other species-poor functional groups include macrofaunal shredders of organic matter (e.g., millipedes) and bioturbators of soils, which include various types of earthworms and termites.

Three Great ‘‘Domains’’ of Organisms on Earth All of life exists in three great ‘‘kingdoms,’’ or domains. These domains are (1) the Bacteria (eubacteria), which are the bacteria as generally considered; (2) Archaea (archaebacteria), which include the methanogens (methane-producers), most extreme halophiles (ones living in hypersaline environments), and hyperthermophiles (ones living in volcanic hot springs, and in mid-sea ocean hot-water vents); and (3) Eucarya (eukaryotes) (Figure 4). The first two domains are prokaryotes, which are unicellular organisms, lacking a unit membranebound nucleus and other organelles, usually having their DNA in a single circular molecule. Eukaryotes, in comparison, consist of all of the organisms that have a unit membranebound nucleus and other organelles, such as mitochondria (Woese et al., 1990). Eukaryotic organisms are often multicellular. This scheme is based on an increasing body of evidence from ribosomal RNA (rRNA) phylogenies, that the archaebacteria are worthy of the same taxonomic status as eukaryotes and bacteria. As shown in Figure 4, the universal

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rRNA tree develops from a postulated ‘‘cenancestor,’’ leading to the relative positions of the three great domains (Pace, 2009).

Number of Species of Prokaryotes Recent estimates of the number of prokaryotic species range from 100,000 to 10 million. Interestingly, the number of species of bacteria so far described in soil amount only to about 4000. This discrepancy is largely due to the fact that only a small proportion, usually less than 1%, of the bacteria present in soil or any other medium are amenable to culturing and subsequent microscopic observation. Most taxonomic descriptions of prokaryotes are made using some variants of 16S rRNA probing, using molecular techniques. It should be noted that, on the basis of the accepted criterion for separating taxa in microbial studies, which is greater than 70% DNA homology, a mouse and a human would be considered as being in the same species. This leads to complications, as we shall see, in discussing the total amount of genetic diversity of all organisms, including the yet largely unknown diversity of Archaea and Eubacteria. The latter now are estimated to have an array of 100 phyla, which are genetically as diverse as the phyla in Animalia, Plantae, and Fungi in older classification systems.

Biomass, Diversity, and Numbers of Bacterial Species on Earth The Bacterial biomass and numbers are often vastly underestimated. We are currently delineating the overall genetic makeup of isolates taken from soils, which are determined by the use of molecular probes. The total numbers of bacteria on earth in all habitats are truly staggering: 4–6 1030 cells, or 350–550 petagrams of carbon (Whitman et al., 1998). One petagram is 1015 g, or 1 billion metric tons. The number of bacteria that are calculated to exist in soils is approximately 2.6 1029 cells, or about 5% of the total on earth. A majority of bacteria exist in oceanic and terrestrial subsurfaces, especially in the deep mantle regions, extending several kilometers below the earth’s surface. Knowledge of the diversity of archaea and bacteria is still limited, but with the use of new massive parallel sequencing devices (Roche 454 and other pyrosequencing techniques), we are beginning to approach an understanding of the very large biodiversity of these organisms. More than one full decade into the ‘‘genomic era,’’ it is necessary to consider a bacterial species as described by its pan-genome, which is comprised of a ‘‘core genome’’ containing genes common in all strains and a ‘‘dispensable genome,’’ containing genes present in two or more strains and genes unique to only one or two unique strains. In essence, the pan-genome of the bacterial domain is of nearly infinite size. For example, in eight genomes representative of the serogroup diversity among group B Streptococcus (GBS) strains, the pan-genome contains 2713 genes, of which 1806 belong to the core genome and 907 belong to the dispensable genome. The GBS pan-genome is predicted to grow by an average of 33 new genes every time a new strain is sequenced. However, this pattern does not hold for all bacterial species. Metagenomics encompasses the full array of microorganisms present in an ecosystem at any point of time (Dinsdale et al., 2008). Metatranscriptomics refers to the number of microbes in a given community or ecosystem that are respiring or



Eucarya Animals

Fungi Plants

Archaea

Entamoeba Euryarchaeota

Euglena

Crenarchaeota

Korarchaeota

Bacteria

Kinetoplasta (e.g., Trypanosoma)

High G+C gram Low G+C gram positives positives / − purples

Parabasalia (e.g., Trichomonas)

− purples and mitochondria

“Archezoa” Microsporidia [?] (e.g., Nosema)

/ − Purples Spirochaetes Fusobacteria

Metamonda (e.g., Giardia)

Thermotogales

Flexibacter/bacteriodes Cyanobacteria and chloroplasts Thermus Aquifex

“Cenancestor” Figure 4 Schematic drawing of a universal rRNA Tree of Life showing the relative positions of groups in the domains Bacteria, Archaea, and Eucarya. The location of the root (the cenancestor) corresponds to that proposed by reciprocally rooted gene phylogenies. (Branch lengths have no meaning in this tree.)

synthesizing at a given time. At any given moment, an estimated 1030 bacterial and archaeal genes are mediating essential ecological processes throughout the world (Moran, 2009).

Viruses are quasiorganisms, not included in the three domains. Viruses are RNA or DNA molecules contained within the protein envelopes. Viral particles are metabolically inert, carrying out neither biosynthetic nor respiratory functions. They multiply only within the host cells, by inducing a living host cell to produce the necessary viral components. Once assembled, the replicated viruses escape from the cells. Viruses infect all sorts of animals, plants, and microbes. Viruses parasitizing bacterial cells are commonly called bacteriophages, or simply phages. Although little is known about the ecology of viruses, they can persist in soils for many years and decades. Some research on viruses in deserts showed that they were inactivated in soils at acid pH levels between 4.5 and 6. There is little information on the overall species diversity of viruses in soils. Current estimates are 5000 species known and perhaps 130,000 in existence. Considerable new knowledge of virus ecology is being gained in aquatic realms: limnology and oceanography. Very little is known about viruses and their ecology in soils, despite their known effects on beneficial bacteria and soil-borne plant pathogens and horizontal gene transfer (transduction). Estimates from 5% to 25% of the carbon fixed by primary producers enter into the microbial loop via virus-induced lysis at

Viruses Grazing food chain

Viruses as Quasiorganisms

Carnivores

Microbial loop

3−15% 1% Grazers

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6−26% Viral loop

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Primary producers 100%

Heterotrophic prokaryotes

Inorganic nutrients

Figure 5 Pelagic food chain model and virus-mediated carbon flow (Reproduced from Kimura M, Jia Z-J, Nakayama N, and Asakawa S (2008) Review–Ecology of viruses in soils: Past, present and future perspectives. Soil Science & Plant Nutrition 54: 1–32, with permission from Wiley.). The dotted lines show virus-mediated pathways. All values are based on the flux of carbon fixed by primary producers (100%).

various trophic levels in the aquatic environments (Figure 5). Despite the concerns about the amount of viral adsorption to soil particles, particularly clays, the greater physical and chemical diversity of soils makes it possible that viruses have an even larger potential to play roles that are similar to those in the aquatic environments.


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Figure 6 Map of the Marseillevirus chromosome. Rings correspond to genome coordinates in kilobases, proteins and protein-coding genes. The pie chart inside the ring represents taxonomic breakdown of Marseillevirus genes by probable origins inferred by phylogenetic analysis or sequence conservation. NCLDV, nucleocytoplasmic large DNA virus of eukaryotes. Reproduced from Kimura M, Jia Z-J, Nakayama N, and Asakawa S (2008) Review – Ecology of viruses in soils: Past, present and future perspectives. Soil Science & Plant Nutrition 54: 1–32.

Because there are an estimated 1031 phages on the planet and they can move between environments, the potential reservoir of genes that can be transferred both locally and globally by phage is enormous. There is little restriction to the types of genes carried by the viral community, suggesting that they influence a wide range of processes, including biogeochemical cycling, short-term adaptation, and long-term evolution of microbes. Recent molecular studies of mechanisms to fend off phages and other forms of invasive DNA, including clustered regularly interspaced short palindromic repeats are increasing the ways in which we can quantify phage and prokaryotic interactions. Although the current usage of phages in soil biological control studies has focused primarily on the plantpathogenic bacteria, the existence of consortia in which insects, bacteria, and viruses interact in a complex five-way mutualistic symbiosis is a proof that interactive complexities exist and are worth exploring. The time scale of viral evolution and the diversity of viral linkages that emerged during that extended time period would explain why the viral-specific genes probably outnumber the cellular ones in metagenomic studies, which forms a very large reservoir of molecular diversity.

As an example of virus–microbial–eucarya interactions, consider the giant Marseillevirus, a previously uncharacterized giant virus of amoebae. The genome repertoire of the virus is composed of nucleocytoplasmic large DNA viruses (NCLDV), core genes and genes apparently obtained from eukaryotic hosts (Boyer et al., 2009, Figure 6). There is a distinct possibility that amoebae are ‘‘melting pots’’ of microbial evolution where diverse forms emerge, including giant viruses with complex genetic repertoires of various origins.

Numbers and Biodiversity of Eukaryotes Fungal Diversity Fungi are multicellular eukaryotes that are found in many habitats worldwide. They have long, ramifying strands (hyphae), which can grow into and explore many microhabitats, and are used for obtaining water and nutrients. The hyphae secrete a considerable array of enzymes, such as cellulases, and even lignases in some specialized forms, decomposing substrates in situ, imbibing the decomposed subunits and translocating them back through the hyphal network. Fungi are abundant, particularly in undisturbed forest floors in which literally thousands of kilometers of hyphal filaments will occur per gram of leaf litter.


Table 1


Comparison of the numbers of known and estimated total species globally of selected groups or organisms

Group

Known species

Estimated total species

Percentage known

Vascular plants Bryophytes Algae Fungi Bacteria Viruses

220,000 17,000 40,000 69,000 3000 5000

270,000 25,000 60,000 1,500,000 30,000 130,000

81 68 67 5 10 4

Source: Reproduced from Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance and conservation. Mycological Research 95: 641–655.

Fungi are still little-described, with possibly less than 5% of them known to science (69,000 described; perhaps 1,500,000) in existence (Table 1). This is largely because of the fact that so many fungi are associated with tropical plants and animals, and these in turn have not been described. As noted at the beginning of this section the roles of mycorrhizas in soil systems are being increasingly viewed as central to much of terrestrial ecosystem function. The total number of mycorrhizal species may be just a few thousand, but they are essential to the growth and reproduction of numerous families of plants (van der Heijden et al., 1998). Recent experimental studies have noted that species richness, namely with large versus small numbers of species of Arbuscular mycorrhiza, has a positive impact on plant primary production in macrocosms of North American old fields (fields undergoing succession and not intensively managed) (Harrison, 1997). Microfauna The unicellular eukaryotes, or Protoctista, include a wide range of organisms, which are more often called protists, or protozoans. These include the flagellates, naked amoebae, testacea, and ciliates (Figure 7). These organisms range in size from a few cubic micrometers in volume to larger ciliates, which may be up to 500 mm in length and 20–30 mm in width. Protozoa are quite numerous, reaching densities of 100,000–200,000 per gram of soil. Bacteria, their principal prey, often exist in numbers up to 1 billion per gram of soil. All of these organisms are true waterfilm dwellers and become dormant or inactive during episodes of drying in the soil. They can exist in inactive or resting stages for literally decades at a time in very xeric environments. About 40,000 extant protozoan species have been described, but many more undoubtedly are awaiting scientific discovery. In an extensive survey of soils from Africa, Australia, and Antarctica, in some cases nearly half of the total species described were new to science. This was particularly true in Africa, where of the 507 species identified, 240 of them, or 47%, were previously undescribed. Even in a more extensively investigated region, Australia, 43% of the total of 361 species were new to science. In Antarctica, 95 species were described, with only 14% or 15%, being unknown. Because many habitats have not yet been investigated, and the isolation procedures are still imperfect, 70–80% of all soil ciliates may yet be unknown. This high proportion may hold true for the other protozoan groups as well. Mesofauna Nematodes Nematodes feed on a wide range of foods. A general trophic grouping is bacterial feeders, fungal feeders,

plant feeders, and predators and omnivores. Anterior (stomal or mouth) structures can be used to differentiate general feeding or trophic groups. The feeding categories are a good introduction, but feeding habits of many genera are complex or poorly known. For example, some genera in immature phases will feed on bacteria and then become predators on other fauna once they have matured. Because of the wide range of feeding types and the fact that nematodes seem to reflect ages of the systems in which they occur (e.g., annual vs. perennial crops, or old fields and pastures and more mature forests), they have been used as indicators of the overall ecosystem condition. As nematodes use a diverse range of food resources it is logical that their feeding, activity, and population dynamics will interact with other components of the ecosystem. For perhaps a century nematodes were almost exclusively regarded as pathogens having adverse effects on plant and animal production. Realization of their wider contributions to ecosystem processes developed in the 1970s, as did shifts toward managing rather than controlling populations of economically important parasites of plants and livestock and the use of nematodes as biocontrol agents for insects. This is a growing area of research in soil ecology, and one in which the intersection of community analysis and ecosystem function could prove very fruitful. Current species of nematodes described total around 5000, and more than 20,000 may exist. For additional information on the activities of these diverse creatures, see Yeates (2010). Collembola Collembolans, or ‘‘springtails,’’ are the primitive Apterygote (wingless) insects. They are called ‘‘springtails’’ because many of them have a spring-like lever, or furcula, which enables them to move many body lengths away from predators by using it in a springing fashion. Collembolans are ubiquitous members of the soil fauna, often reaching abundances of 100,000 or more per square meter. They occur throughout the soil profile, where their major diet is decaying vegetation and associated microbes (usually fungi). However, like many members of the soil fauna, collembolans defy placement in exact trophic groups. Many collembolan species will eat nematodes when those are abundant. Some feed on live plants or their roots. One family (Onychiuridae) may feed in the rhizosphere and ingest mycorrhizae or even plantpathogenic fungi. Eight families of Collembolans occur in soils. Many Collembolans are opportunistic species, capable of rapid population growth under suitable conditions. Eggs are laid in groups. Collembolans become sexually mature with the fifth


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Figure 7 Morphology of four types of soil Protozoa: (a) flagellate (Bodo), (b) naked amoeba (Naegleria), (c) testacean (Hyalosphenia), and (d) ciliate (Oxytricha). Reproduced from Coleman DC, Crossley Jr. DA, and Hendrix PF (2004) Fundamentals of Soil Ecology. San Diego: Academic Press.

or sixth instar, but they continue to molt throughout their life. Although many species are bisexual, some of the common species are parthenogenic, consisting of females only. Collembolan ‘‘blooms’’ are a phenomenon of late winter or early spring, when some species may appear in large numbers on the surface of snow banks, on the surface ice of pond water, or on lichen-covered granite outcrops. There are some 6500 described species and possibly more than 10,000 in existence. Mites (Acari) The soil mites, Acari, are chelicerate arthropods related to the spiders. They are often the most abundant microarthropods in many types of soils. A 100 g sample may contain as many as 500 mites representing nearly 100 genera. This diverse array includes participants in three or more trophic levels, with varied strategies for feeding, reproduction, and dispersal.

Four suborders of mites occur frequently in soils: the Oribatei, Prostigmata, Mesostigmata, and Astigmata. Occasionally, mites from other habitats are extracted from soil samples. These include, for example, plant mites (also called spider mites), predaceous mites normally found on green vegetation, and parasites of vertebrates or invertebrates. The most numerous ones are the true soil mites. The oribatid mites (Oribatei) are the characteristic mites of the soil and are usually fungivorous or detritivorous. Oribatid mites are very speciose, numbering 20,000 known species, with perhaps 60,000 yet to be described. A widespread assumption in the soil ecology literature has been that the oribatids feed on fungi of decomposing leaf and root litter, hence may have narrow niche overlaps in food items they consume. Recent studies in Europe have demonstrated a somewhat wider range of food items in oribatid diets that have been measured by the



stable isotope ratios (15N/14N). A total of four feeding guilds among 36 species or taxa were differentiated. In temperate deciduous and tropical forests, the Oribatids are very speciose. One notable example of high temperate zone oribatid diversity is that up to 170 species occur in just a few hundred square meters of the forest floor of a mesic, mixed deciduous forest watershed in western North Carolina. This species richness, or a-diversity (the diversity within a given site), exceeds that of some tropical forest oribatids. In a field study, species richness of oribatids declined with decreased litter species richness in experimental (1 m2) enclosures from five down to one species of deciduous tree litter. The decline in oribatid species richness was attributed to the lower physical and chemical diversity of the available microhabitats from polyspecific to oligospecific litters, including leaf petioles, which specialized feeders such as phthiracarid (‘‘box’’) mites would occupy preferentially. Impacts of oribatid mites farther up the food chain, in ways not often considered by soil ecologists, have been demonstrated recently. In tropical America and probably in the tropics more generally, oribatids as a group contain as many as 80 alkaloids and represent a major dietary source of alkaloids in poison frogs. A conservative assumption is that they accumulate alkaloids from their food sources. To what extent do fungi or other organisms contribute alkaloids to the oribatids’ diet? Mesostigmatid mites are nearly all predators on other small fauna, although a few species are fungivores and may become numerous at times. 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. Very little is known of the niches or ecological requirements of most soil mite species, but some interesting information is emerging. For further details on the life-history characteristics of these interesting animals, see Coleman et al. (2004). About 20,000 species have been described and possibly more than 80,000 exist. Macrofauna Termites Termites (Isoptera) are one of the major ecosystem ‘‘engineers’’ particularly in tropical regions. Termites are social insects with a well-developed caste system. By their ability to digest wood, they have become economic pests of major importance in some regions of the world. Termites are arranged in five different families. The termites in a more primitive family, the Kalotermitidae, possess a gut flora of protozoans, which enables them to digest cellulose. Their normal food is wood that has come into contact with soil. Many species of termites construct runways of soil, or along root channels, and some are builders of large, spectacular mounds. Members of the phylogenetically advanced family Termitidae possess a formidable array of microbial symbionts (bacteria and fungi, but not protozoa), which enable them to process and digest the humified organic matter in tropical soils and to grow and thrive on such a diet. Although termites are mainly tropical in distribution, they occur in temperate zones and deserts as well. Termites are often considered the tropical analogs of earthworms since they reach large abundances in the tropics and process large amounts of litter. Termites parallel earthworms in ingestive and soil turnover functions. The principal difference is that the

earthworms egest much of what they ingest in an altered form (that enriches microbial action), whereas termites can transfer large amounts of soil or organic material into building nests and mounds (carbon sinks). More than 2000 species of termites have been described, and probably up to 10,000 exist. Earthworms The earthworm fauna of North America is surprisingly poorly known, given the importance of these animals to soil processes and soil structure. Much of the evidence for earthworm effects on soil processes comes from agroecosystems and involves a small group of European lumbricids (family Lumbricidae in the order Oligochaeta). In North America, south of the southern limit of the Wisconsinan glaciation, several native genera exist. However, exotic (often peregrine European lumbricids) earthworm species have been introduced into much of this area following human population changes and colonizations. Impacts of the exotic earthworms on native species are not well understood, although there is evidence that when native habitat is destroyed and native earthworm species extirpated, exotic earthworms colonize the newly empty habitat. As more extensive studies are carried out, it is becoming clear that earthworms are present in a wide variety of tropical as well as temperate ecosystems. Earthworms play important roles in the fragmentation, breakdown, and incorporation of soil organic matter (SOM). This affects the distribution of SOM and also its chemical and physical characteristics. Changes in any of these soil parameters may have significant effects on other soil biota, by changing their resource base (e.g., distribution and quality of SOM, microbes, or small soil fauna) or by changing the physical structure of the soil. Recent evidence indicates that earthworm activities impact the communities of other soil biota through their effects on the chemical and physical characteristics of SOM, causing changes in the oribatid species richness and microarthropod abundances. It is probable that earthworminduced changes in the microbial and microarthropod communities will also have impacts both higher and lower in the soil food web. Some 3650 species of earthworms have been described and possibly as many as 8000 exist.

Levels of Disturbance; Effects on Biodiversity The impact of invasive species on plants and soil organisms is a subset of a more general phenomenon: the effects of various levels of disturbance on soil biodiversity. Several recent studies have shown little support for optimization of local soil animal diversity at intermediate levels of disturbance. In fact, a wide range of disturbances of soil by tillage could strongly elevate or reduce macrofaunal group diversity, but the diversity of microfauna was little affected. Apparently the magnitude of these effects depends on soil type, climate, and tillage operation. The overall consensus seems to be that in conversion from natural vegetation to agriculture, the diversity of a wide range of microbial communities and faunal groups, ranging from nematodes to earthworms and termites, is significantly reduced in the disturbed agroecosystems. Rigorous experimental testing of the disturbance–diversity relationship is still needed to ascertain its importance as a regulator of belowground diversity. We must keep in mind the spatio-temporal


aspects of soil communities. Thus enhanced habitat complexity and diversity of available food resources will support localized ‘‘hot spots’’ of more diverse faunal communities. A more general aspect of disturbance studies is that related to land use and global change phenomena (Wall, 2004).

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See also: Archaea, Origin of. Eukaryotes, Origin of. Food Webs. Fungi. Nitrogen, Nitrogen Cycle. Soil Conservation

References Conclusions It is apparent that a large proportion of the biota associated with soils is as yet undescribed, with the most extreme cases being the bacteria and fungi. However, of even the somewhat more extensively studied groups, such as the oribatid mites, more than half remain unknown to science. Therefore, it is premature to give even a rough estimate of the total numbers of species that occur in many of these taxa; as such large percentages of the total number of organisms are still unknown. When considering the diverse array of many kingdoms in all three domains of the biota, there are ample causative factors for the impressively large biodiversity observed in soils. These factors encompass many physically distinct microhabitats, organismal phenologies, numerous legacy effects, including stabilizing effects of SOM, and facilitation effects from many mutualistic interactions. In addition to the highly heterogeneous environment, a high degree of omnivory prevails in resource-use among the decomposer organisms, tending to reduce competition, and hence plays a major role in explaining the high degree of functional complementarity in decomposer communities. This is another way of considering soils as organizing centers in the terrestrial ecosystems (see Soils as Organizing Centers in Ecosystems). It is incumbent on the rising generation of ecologists and biologists to develop more innovative ways to describe, catalog, and understand the myriad patterns and processes in the biosphere, which are due in large part to the actions of the biota. It is hoped that some of the observations in this article, plus the insights offered by the references listed will encourage this effort.

Appendix List of Courses 1. Soil Ecology 2. Terrestrial Ecosystems 3. Global Biodiversity

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