Soil ecology

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Soil ecology studies interactions among soil organisms, and their environment. [1] It is particularly concerned with the cycling of nutrients, soil aggregate formation and soil biodiversity. [2]

Contents

Overview

Soil is made up of a multitude of physical, chemical, and biological entities, with many interactions occurring among them. It is a heterogenous mixture of minerals and organic matter with variations in moisture, temperature and nutrients. Soil supports a wide range of living organisms and is an essential component of terrestrial ecology.

Features of the ecosystem

Soil fauna

Soil fauna is crucial to soil formation, litter decomposition, nutrient cycling, biotic regulation, and for promoting plant growth. Yet soil organisms remain underrepresented in studies on soil processes and in existing modeling exercises. This is a consequence of assuming that much below ground diversity is ecologically redundant and that soil food webs exhibit a higher degree of omnivory. However, evidence is accumulating on the strong influence of abiotic filters, such as temperature, moisture and soil pH, as well as soil habitat characteristics in controlling their spatial and temporal patterns. [18]

Soils are complex systems and their complexity resides in their heterogeneous nature: a mixture of air, water, minerals, organic compounds, and living organisms. The spatial variation, both horizontal and vertical, of all these constituents is related to soil forming agents varying from micro to macro scales. [19] Consequently, the horizontal patchy distribution of soil properties (soil temperature, moisture, pH, litter/nutrient availability, etc.) also drives the patchiness of the soil organisms across the landscape, [20] and has been one of the main arguments for explaining the great diversity observed in soil communities. [21] Because soils also show vertical stratification of their elemental constituents along the soil profile as result of microclimate, soil texture, and resource quantity and quality differing between soil horizons, soil communities also change in abundance and structure with soil depth. [22] [18]

The majority of these organisms are aerobic, so the amount of porous space, pore-size distribution, surface area, and oxygen levels are crucial to their life cycles and activities. The smallest creatures (microbes) use the micropores filled with air to grow, whereas other bigger animals require bigger spaces, macropores, or the water film surrounding the soil particles to move in search for food. Therefore, soil textural properties together with the depth of the water table are also important factors regulating their diversity, population sizes, and their vertical stratification. Ultimately, the structure of the soil communities strongly depends not only on the natural soil forming factors but also on human activities (agriculture, forestry, urbanization) and determines the shape of landscapes in terms of healthy or contaminated, pristine or degraded soils. [18]

Macrofauna

Soil macrofauna, climatic gradients and soil heterogeneity Historical factors, such as climate and soil parent materials, shape landscapes above and below ground, but the regional/local abiotic conditions constraint biological activities. These operate at different spatial and temporal scales and can switch on and off different organisms at different microsites resulting in a hot moment in a particular hotspot. As a result, trophic cascades can occur up and down the food web. Soil invertebrates are shown. Ellipses indicate hot (red) or cold spots (blue), with the curved arrows giving some examples of the factors that could switch on/off a hot moment and the straight black arrows (continuous black line = on, dashed = off) showing the implications for soil processes along the soil profile. In the boxes, the main ecosystem characteristics are listed. Soil fauna, climatic gradients and soil heterogeneity.jpg
Soil macrofauna, climatic gradients and soil heterogeneity 
Historical factors, such as climate and soil parent materials, shape landscapes above and below ground, but the regional/local abiotic conditions constraint biological activities. These operate at different spatial and temporal scales and can switch on and off different organisms at different microsites resulting in a hot moment in a particular hotspot. As a result, trophic cascades can occur up and down the food web.
Soil invertebrates are shown. Ellipses indicate hot (red) or cold spots (blue), with the curved arrows giving some examples of the factors that could switch on/off a hot moment and the straight black arrows (continuous black line = on, dashed = off) showing the implications for soil processes along the soil profile. In the boxes, the main ecosystem characteristics are listed.

Since all these drivers of biodiversity changes also operate above ground, it is thought that there must be some concordance of mechanisms regulating the spatial patterns and structure of both above and below ground communities. In support of this, a small-scale field study revealed that the relationships between environmental heterogeneity and species richness might be a general property of ecological communities. [21] In contrast, the molecular examination of 17,516 environmental 18S rRNA gene sequences representing 20 phyla of soil animals covering a range of biomes and latitudes around the world indicated otherwise, and the main conclusion from this study was that below-ground animal diversity may be inversely related to above-ground biodiversity. [23] [18]

The lack of distinct latitudinal gradients in soil biodiversity contrasts with those clear global patterns observed for plants above ground and has led to the assumption that they are indeed controlled by different factors. [24] For example, in 2007 Lozupone and Knight found salinity was the major environmental determinant of bacterial diversity composition across the globe, rather than extremes of temperature, pH, or other physical and chemical factors. [25] In another global scale study in 2014, Tedersoo et al. concluded fungal richness is causally unrelated to plant diversity and is better explained by climatic factors, followed by edaphic and spatial patterns. [26] Global patterns of the distribution of macroscopic organisms are far poorer documented. However, the little evidence available appears to indicate that, at large scales, soil metazoans respond to altitudinal, latitudinal or area gradients in the same way as those described for above-ground organisms. [27] In contrast, at local scales, the great diversity of microhabitats commonly found in soils provides the required niche portioning to create hot spots of diversity in just a gram of soil. [24] [18]

Spatial patterns of soil biodiversity are difficult to explain, and its potential linkages to many soil processes and the overall ecosystem functioning are debated. For example, while some studies have found that reductions in the abundance and presence of soil organisms results in the decline of multiple ecosystem functions, [28] others concluded that above-ground plant diversity alone is a better predictor of ecosystem multi-functionality than soil biodiversity. [29] Soil organisms exhibit a wide array of feeding preferences, life-cycles and survival strategies and they interact within complex food webs. [30] Consequently, species richness per se has very little influence on soil processes and functional dissimilarity can have stronger impacts on ecosystem functioning. [31] Therefore, besides the difficulties in linking above and below ground diversities at different spatial scales, gaining a better understanding of the biotic effects on ecosystem processes might require incorporating a great number of components together with several multi-trophic levels  [32] as well as the much less considered non-trophic interactions such as phoresy, passive consumption. [33] ) In addition, if soil systems are indeed self-organized, and soil organisms concentrate their activities within a selected set of discrete scales with some form of overall coordination, [34] there is no need for looking for external factors controlling the assemblages of soil constituents. Instead we might just need to recognize the unexpected and that the linkages between above and below ground diversity and soil processes are difficult to predict. [18]

Microfauna

Recent advances are emerging from studying sub-organism level responses using environmental DNA   [35] and various omics approaches, such as metagenomics, metatranscriptomics, proteomics and proteogenomics, are rapidly advancing, at least for the microbial world. [36] Metaphenomics has been proposed recently as a better way to encompass the omics and the environmental constraints. [37] [18]

Soil microbes

Soil harbors many microbes: bacteria, archaea, protist, fungi and viruses. [38] A majority of these microbes have not been cultured and remain undescribed. [39] Development of next generation sequencing technologies open up the avenue to investigate microbial diversity in soil. [40] One feature of soil microbes is spatial separation which influences microbe to microbe interactions and ecosystem functioning in the soil habitat. [41] Microorganisms in soil are found to be concentrated in specific sites called 'hot spots' which is characterized by an abundance of resources such as moisture or nutrients. [42] An example is the rhizosphere, and areas with accumulated organic matter such as the detritusphere. [43] These areas are characterized by the presence of decaying root litter and exudates released from plant roots which regulates the availability of carbon and nitrogen and in consequence modulate microbial processes. [43] Apart from labile organic carbon, spatial separation of microbes in soil may be influenced by other environmental factors such as temperature and moisture. [44] Other abiotic factors like pH and mineral nutrient composition may also influence the distribution of microorganisms in soil. [45] Variability of these factors make soil a dynamic system. [46] Interactions between members of the soil microhabitat takes place via chemical signaling which is mediated by soluble metabolites and volatile organic compounds, in addition to extracellular polysaccharides. [47] Chemical signals enable microbes to interact, for example bacterial peptidoglycans stimulate growth of Candida albicans. [48] Reciprocally, C. albicans production of farnesol modulates the expression of virulence genes and influences bacterial quorum sensing. [49] Trophic interactions by microbes in the same environment is driven by molecular communication. [50] Microbes may also exchange metabolites to support each other's growth, e.g., the release of extracellular enzymes by ectomycorrhiza decomposes organic matter and releases nutrients which then benefits other members of the population, in exchange organic acids from bacteria stimulate fungal growth [51] These examples of trophic interactions especially metabolite dependencies drive species interactions and are important in the assembly of soil microbial communities. [52]

Soil food web

Diverse organisms make up the soil food web. They range in size from one-celled bacteria, algae, fungi, and protozoa, to more complex nematodes and micro-arthropods, to the visible earthworms, insects, small vertebrates, and plants. As these organisms eat, grow, and move through the soil, they make it possible to have clean water, clean air, healthy plants, and moderated water flow.

There are many ways that the soil food web is an integral part of landscape processes. Soil organisms decompose organic compounds, including manure, plant residues, and pesticides, preventing them from entering water and becoming pollutants. They sequester nitrogen and other nutrients that might otherwise enter groundwater, and they fix nitrogen from the atmosphere, making it available to plants. Many organisms enhance soil aggregation and porosity, thus increasing infiltration and reducing surface runoff. Soil organisms prey on crop pests and are food for above-ground animals.

Research

Research interests span many aspects of soil ecology and microbiology, Fundamentally, researchers are interested in understanding the interplay among microorganisms, fauna, and plants, the biogeochemical processes they carry out, and the physical environment in which their activities take place, and applying this knowledge to address environmental problems.

Example research projects are to examine the biogeochemistry and microbial ecology of septic drain field soils used to treat domestic wastewater, the role of anecic earthworms in controlling the movement of water and nitrogen cycle in agricultural soils, and the assessment of soil quality in turf production. [53]

Of particular interest as of 2006 is to understand the roles and functions of arbuscular mycorrhizal fungi in natural ecosystems. The effect of anthropic soil conditions on arbuscular mycorrhizal fungi, and the production of glomalin by arbuscular mycorrhizal fungi are both of particular interest due to their roles in sequestering atmospheric carbon dioxide.

Related Research Articles

<span class="mw-page-title-main">Ecosystem</span> Community of living organisms together with the nonliving components of their environment

An ecosystem is a system that environments and their organisms form through their interaction. The biotic and abiotic components are linked together through nutrient cycles and energy flows.

<span class="mw-page-title-main">Soil</span> Mixture of organic matter, minerals, gases, liquids, and organisms that together support life

Soil, also commonly referred to as earth, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support the life of plants and soil organisms. Some scientific definitions distinguish dirt from soil by restricting the former term specifically to displaced soil.

<span class="mw-page-title-main">Mangrove</span> Shrub growing in brackish water

A mangrove is a shrub or tree that grows mainly in coastal saline or brackish water. Mangroves grow in an equatorial climate, typically along coastlines and tidal rivers. They have particular adaptations to take in extra oxygen and remove salt, allowing them to tolerate conditions that kill most plants. The term is also used for tropical coastal vegetation consisting of such species. Mangroves are taxonomically diverse due to convergent evolution in several plant families. They occur worldwide in the tropics and subtropics and even some temperate coastal areas, mainly between latitudes 30° N and 30° S, with the greatest mangrove area within 5° of the equator. Mangrove plant families first appeared during the Late Cretaceous to Paleocene epochs and became widely distributed in part due to the movement of tectonic plates. The oldest known fossils of mangrove palm date to 75 million years ago.

<span class="mw-page-title-main">Microbial ecology</span> Study of the relationship of microorganisms with their environment

Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses. This relationship is often mediated by secondary metabolites produced my microorganism. These secondary metabolites are known as specialized metabolites and are mostly volatile or non volatile compounds. These metabolites include terpenoids, sulfur compounds, indole compound and many more.

<span class="mw-page-title-main">Soil food web</span> Complex living system in the soil

The soil food web is the community of organisms living all or part of their lives in the soil. It describes a complex living system in the soil and how it interacts with the environment, plants, and animals.

<span class="mw-page-title-main">Rhizosphere</span> Region of soil or substrate comprising the root microbiome

The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microorganisms that feed on sloughed-off plant cells, termed rhizodeposition, and the proteins and sugars released by roots, termed root exudates. This symbiosis leads to more complex interactions, influencing plant growth and competition for resources. Much of the nutrient cycling and disease suppression by antibiotics required by plants occurs immediately adjacent to roots due to root exudates and metabolic products of symbiotic and pathogenic communities of microorganisms. The rhizosphere also provides space to produce allelochemicals to control neighbours and relatives.

<span class="mw-page-title-main">Microbial loop</span> Trophic pathway in marine microbial ecosystems

The microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

<span class="mw-page-title-main">Soil carbon</span> Solid carbon stored in global soils

Soil carbon is the solid carbon stored in global soils. This includes both soil organic matter and inorganic carbon as carbonate minerals. It is vital to the soil capacity in our ecosystem. Soil carbon is a carbon sink in regard to the global carbon cycle, playing a role in biogeochemistry, climate change mitigation, and constructing global climate models. Microorganisms play an important role in breaking down carbon in the soil. Changes in their activity due to rising temperatures could possibly influence and even contribute to climate change. Human activities have caused a massive loss of soil organic carbon. For example, anthropogenic fires destroy the top layer of the soil, exposing soil to excessive oxidation.

Soil biodiversity refers to the relationship of soil to biodiversity and to aspects of the soil that can be managed in relative to biodiversity. Soil biodiversity relates to some catchment management considerations.

In ecology, the term productivity refers to the rate of generation of biomass in an ecosystem, usually expressed in units of mass per volume per unit of time, such as grams per square metre per day. The unit of mass can relate to dry matter or to the mass of generated carbon. The productivity of autotrophs, such as plants, is called primary productivity, while the productivity of heterotrophs, such as animals, is called secondary productivity.

Agricultural microbiology is a branch of microbiology dealing with plant-associated microbes and plant and animal diseases. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations. The primary goal of agricultural microbiology is to comprehensively explore the interactions between beneficial microorganisms like bacteria and fungi with crops. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations.

Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.

Microbial biogeography is a subset of biogeography, a field that concerns the distribution of organisms across space and time. Although biogeography traditionally focused on plants and larger animals, recent studies have broadened this field to include distribution patterns of microorganisms. This extension of biogeography to smaller scales—known as "microbial biogeography"—is enabled by ongoing advances in genetic technologies.

<span class="mw-page-title-main">Root microbiome</span> Microbe community of plant roots

The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.

<span class="mw-page-title-main">Microbiome</span> Microbial community assemblage and activity

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs, the first pronouncing the dynamic character of the microbiome, and the second clearly separating the term microbiota from the term microbiome.

<span class="mw-page-title-main">Mycoplankton</span> Fungal members of the plankton communities of aquatic ecosystems

Mycoplankton are saprotrophic members of the plankton communities of marine and freshwater ecosystems. They are composed of filamentous free-living fungi and yeasts that are associated with planktonic particles or phytoplankton. Similar to bacterioplankton, these aquatic fungi play a significant role in heterotrophicmineralization and nutrient cycling. Mycoplankton can be up to 20 mm in diameter and over 50 mm in length.

<span class="mw-page-title-main">Soil regeneration</span> Creation of new soil and rejuvenation of soil health

Soil regeneration, as a particular form of ecological regeneration within the field of restoration ecology, is creating new soil and rejuvenating soil health by: minimizing the loss of topsoil, retaining more carbon than is depleted, boosting biodiversity, and maintaining proper water and nutrient cycling. This has many benefits, such as: soil sequestration of carbon in response to a growing threat of climate change, a reduced risk of soil erosion, and increased overall soil resilience.

Bioremediation of petroleum contaminated environments is a process in which the biological pathways within microorganisms or plants are used to degrade or sequester toxic hydrocarbons, heavy metals, and other volatile organic compounds found within fossil fuels. Oil spills happen frequently at varying degrees along with all aspects of the petroleum supply chain, presenting a complex array of issues for both environmental and public health. While traditional cleanup methods such as chemical or manual containment and removal often result in rapid results, bioremediation is less labor-intensive, expensive, and averts chemical or mechanical damage. The efficiency and effectiveness of bioremediation efforts are based on maintaining ideal conditions, such as pH, RED-OX potential, temperature, moisture, oxygen abundance, nutrient availability, soil composition, and pollutant structure, for the desired organism or biological pathway to facilitate reactions. Three main types of bioremediation used for petroleum spills include microbial remediation, phytoremediation, and mycoremediation. Bioremediation has been implemented in various notable oil spills including the 1989 Exxon Valdez incident where the application of fertilizer on affected shoreline increased rates of biodegradation.

<span class="mw-page-title-main">Viral shunt</span>

The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.

Saprotrophic bacteria are bacteria that are typically soil-dwelling and utilize saprotrophic nutrition as their primary energy source. They are often associated with soil fungi that also use saprotrophic nutrition and both are classified as saprotrophs.

References

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